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2. Significance Criteria

The project impacts to biological resources discussed below have been evaluated based upon the Significance Criteria specifically developed for this EIR. The SMP includes a comprehensive mitigation package, including compensatory mitigation where impacts to resources cannot be avoided. The District recognizes that some of these impacts may not be at a level of significance to require mitigation. To be consistent with its mission to protect and enhance natural resources, and to resolve controversy over what level of mitigation is required, the District has decided for the SMP to nevertheless provide compensatory mitigation for wetland and riparian impacts due to sediment removal and vegetation management that cannot be avoided or minimized. This commitment goes beyond the level of mitigation implied by some of the thresholds below. The Significance Criteria for impacts to biological resources are provided in the list that follows. For ease of reference in the impacts discussion, each major criterion is numbered.

Would the project:

a. Sensitive Plant Communities

Criterion Bio-1 Have a substantial permanent adverse effect on wetland, riparian, or other sensitive habitat identified in local or regional plans, policies or regulations, or by the California Department of Fish and Game, U.S. Fish and Wildlife Service, or National Marine Fisheries Service, including:

-- Result in an adverse effect on wetlands as defined by Section 404 of the Clean Water Act (including, but not limited to marsh, vernal pool, or tidal or seasonal wetlands) through direct permanent removal or filling of wetlands, hydrological interruption, or other actions that reduce the function and value of the habitat. Considerations include significance of the habitat, presence of endangered or threatened species, water quality, and other wetland functions.

-- Result in an adverse effect on riparian vegetation or other sensitive habitat in relation to remaining existing habitat in the region or result in substantial fragmentation or isolation of sensitive habitat.

Criterion Bio-2 Threaten to eliminate a plant community from the region. [Mandatory Finding of Significance]

Criterion Bio-3 Result in removal of a heritage sized tree (18 inches or greater dbh) unless it poses an imminent threat/danger to people or property.

Criterion Bio-4 Introduce invasive plant species into native, riparian, or wetland habitat areas where native species could become displaced or the genetic integrity of the native ecosystem could be degraded.

b. Wildlife

Criterion Bio-5 Result in substantial reduction in habitat for wildlife species. [Mandatory Finding of Significance] This impact includes "substantial" reduction of the habitat currently or potentially occupied on a year-round or seasonal basis by native resident or migratory species but does not apply to a "vagrant" species, which is defined as an individual that has strayed from its typical migration route. Effects to be considered include:

-- Would the reduction in habitat cause a wildlife population to drop below self-sustaining levels. [Mandatory Finding of Significance] i.e., Would the viability of an existing population be threatened or jeopardized due to the amount of habitat removed. This includes an action that isolates a population of a species from other populations with which it normally breeds.

-- Would the reduction in habitat result in a permanent reduction in feeding, breeding, or resting areas for a large number of resident and regularly occurring wildlife species and/or an impediment of the use of native wildlife nursery sites.

-- Would the reduction in habitat interfere substantially with the movement of any native resident or migratory wildlife species or with established native resident or migratory wildlife corridors by blocking access, fragmenting access, or permanently eliminating known wildlife corridors.

Criterion Bio-6 Threaten to eliminate an animal community from the region. [Mandatory Finding of Significance]

Criterion Bio-7 Introduce invasive wildlife species into native, riparian, or wetland habitat areas where native species could become displaced or the genetic integrity of the native ecosystem could be degraded.

Criterion Bio-8 Directly harm nesting species protected under the provisions of the Migratory Bird Treaty Act, including take of migratory birds or their occupied nests, eggs, or young.

c. Fisheries/Aquatic Habitat

Criterion Bio-9 Result in substantial reduction in habitat for fish or otherwise cause a fish population to drop below self-sustaining levels. [Mandatory Finding of Significance]

Criterion Bio-10 Substantially interfere with migration, spawning, incubating, or rearing habitat for native aquatic species. Considerations for all of the above include whether or not a project would substantially:

-- Create barriers to fish migration, including alterations that increase velocities that fish cannot overcome;

-- Reduce streamflows such that they fail to meet specific lifestage flow recommendations or needs;

-- Result in loss of Shaded Riverine Aquatic (SRA) cover habitat;

-- Cause a change in temperature that would affect the success of any lifestage (including loss of vegetation that provides over-water shade);

-- Degrade channel substrate that is important for providing fish habitat (including loss of spawning gravels);

-- Change geomorphological processes such as sediment transport, erosion, or sheer stress on substrate and vegetation;

-- Cause changes in instream habitat due to removal or alteration of rocks, woody debris, etc.;

-- Decrease Dissolved Oxygen levels below existing or lethal limits.

Criterion Bio-11 Cause increased turbidity and/or resuspension of toxic pollutants at the site or downstream, substantially affecting aquatic habitat.

d. Special-Status Species

Criterion Bio-12 Have a substantial adverse effect, either directly or indirectly, on any listed, proposed, or candidate endangered or threatened species, listed under either the California or Federal Endangered Species Acts, including: reducing the number or restricting the range of a threatened or endangered plant or animal. [Mandatory Finding of Significance] This includes any activity that would kill, harm, or result in chronic disturbance of a listed species or result in a significant reduction in the species' population or habitat.

Criterion Bio-13 Have a substantial adverse effect, either directly or indirectly, on any species identified as a special-status plant or wildlife species, including: any activity that will kill, harm, remove habitat for, or result in chronic disturbance of a species listed by the California Department of Fish and Game as a "Species of Special Concern," or included on List 1 or 2 of the California Native Plant Society's Inventory of Rare and Endangered Vascular Plants of California.

Criterion Bio-14 Conflict with provisions of an adopted Habitat Conservation Plan, Natural Community Conservation Plan, or other approved local, regional, or state habitat conservation plan or biological resource preservation policy.

3. Impacts

a. Overview

Sediment removal, vegetation management, and bank protection, the three major stream maintenance activities, would potentially cause significant impacts to biological resources. Numerous other stream maintenance activities that do not fall within the three previously described categories are also included in the SMP as "minor" activities. These activities are listed in the project description. The three major activities and many of the minor activities have the potential to impact biological resources and are thus addressed in this impacts section where relevant.

The assessment of impacts from the SMP are limited to an evaluation of the changes the SMP could cause in the physical environment from the current baseline condition. In the impact discussion below, three general categories of changes are identified: those which will be caused by continuing maintenance over an additional period of 20 years, areas included in the program where routine maintenance has not occurred on a frequent basis in the past, and the resumption of the use of herbicides in the Santa Clara Basin. This impact evaluation does not assess the biological impacts of the original construction of the flood protection projects, nor of prior, longstanding maintenance. Rather, it evaluates the effect of continuing the existing maintenance practices, with some modification in area and methodology, in a new program approach for a length of 20 years.

The SMP includes an extensive array of BMPs (see SMP Appendix H), many of which reduce impacts to biological resources. The BMPs that reduce the impacts to biological resources described below are referenced in the discussion where applicable. Additionally, the SMP includes a mitigation package to compensate for the significant residual impacts to in-stream wetlands and riparian vegetation.

The compensatory mitigation package includes the following 4 components: (1) tidal wetland restoration; (2) freshwater wetland creation; (3) stream and watershed protection; and (4) control of giant reed. This mitigation is described in Chapter 5 and Appendix E of the SMP. The components of the compensatory mitigation package are summarized in Tables II-7, II-8, and II-9 in Chapter II, Project Description, and proposed sites are shown in Figure II-7. Compensatory mitigation measures are referenced in the discussion where applicable.

The compensatory mitigation package was designed to compensate for the same or similar functions as those impacted. Guiding principles were established with the advice of the stakeholders and regulatory agencies to assist in development of the mitigation elements. Some of these guiding principles include: mitigation will match impacts by basin; larger, sustainable sites are preferable to smaller, fragmented sites; creation of freshwater and tidal wetlands must be included as part of the mitigation program; and other mitigation techniques such as invasive species control and land preservation are acceptable. The 4 elements of the compensatory mitigation package are briefly described below:

• The Tidal Wetland Restoration component would establish 30 acres of self-sustaining tidal wetland by restoring a diked salt evaporation pond. The pond is located along South San Francisco Bay, and bordered by Sunnyvale East and West Channels, and Guadalupe Slough.

• The Freshwater Wetland Creation component would create at least 14 acres of freshwater wetlands at Los Capitancillos, Coyote Lakes Park Site 10A, and Church Pond Number 2. These sites are currently either fields of annual grasses or a nonfunctioning percolation pond which would be converted to seasonal or perennial wetlands at locations offstream, but directly adjacent to creeks. The District will continue searching for additional sites for freshwater wetland creation.

• The Stream and Watershed Protection component includes the purchase of approximately 920 to 1210 acres of land and conservation easements to preserve, protect, and improve streams and their associated watersheds in the county. This mitigation component will focus on preservation and improvement of streams that are generally in a fairly undisturbed state and in good ecological condition. This component includes restoration and management actions, where suitable, such as removal of invasive species, and replacement of in-stream road crossings with more environmentally-sensitive crossing.
• The Giant Reed Control component would remove a non-native, invasive plant of riparian areas, giant reed, from 125 acres in the county. This component also includes mapping, revegetation, monitoring, and educational elements.

Additionally, the SMP includes a compensatory mitigation package to compensate for the significant residual impacts of the bank protection program. This mitigation is described in detail in Appendix E of the SMP. The two components of the Programmatic Impact Assessment and Mitigation for Routine Bank Protection Activities are summarized Tables II-8 and II-9.

b. Determination of In-stream Wetland and Woody Riparian Vegetation Impacts

This section describes the approach used to determine impacts to in-stream wetland and woody riparian vegetation from sediment removal and vegetation management. As described in the Project Description, bank protection generally does not directly impact woody riparian vegetation. Any woody riparian vegetation impacts that do occur from bank protection would be determined on a project-specific basis and mitigated according to protocol developed under this program and described in Appendix E of the SMP.

1) Types of Impact

As sediment is removed, so is any vegetation that is growing on it. The type of vegetation removed can consist of freshwater or tidal wetland vegetation, a mix of wetland and herbaceous upland vegetation, or almost entirely upland vegetation depending on the location of the stream channel (e.g., tidal versus freshwater), spatial relationship of the low-flow channel to sediment benches, presence or absence of year-round water, and the duration between and overlap of different types of maintenance activities. The amount of vegetation present can also vary based on these conditions. Vegetation may be absent from areas with dry conditions, such as high sediment benches and ephemeral stream beds.

Channel vegetation management involves the application of herbicide to targeted vegetation or the hand removal of such vegetation. Target vegetation primarily consists of either erect emergent herbaceous wetland vegetation, such as cattails and bulrush, or woody vegetation consisting of native riparian species such as willows and box elder and non-native species such as eucalyptus. The woody riparian vegetation removed is comprised of seedlings and saplings no greater than 2" in diameter at breast height (48"; dbh) for herbicide application and 6" dbh for hand removal methods. Large stature, mature, woody vegetation is not removed.

2) Vegetation Responses to Impacts

District studies have found that wetland vegetation often quickly re-establishes following sediment removal projects. The "Instream Wetland Vegetation Regrowth Study" (Rankin and Hillman 2000) found 65% and 98% average regrowth within one and two years, respectively, after 1997 sediment removal at six non-tidal freshwater study sites. Average regrowth on two tidal study sites was less, at 21% and 29% after one and two years, respectively. The pattern of rapid re-establishment, with greater rates in non-tidal than in tidal areas, was supported by regrowth study results on four additional 1998 sediment removal sites. After one year those sites supported more non-tidal wetland than was present prior to sediment removal and almost 70% of the tidal wetland that was present prior to sediment removal.

Vegetation dominance and quality (as represented by vegetation type, total percent cover of vegetation, and relative percent cover of native and invasive species) were similar between pre- and post-project years on both sediment removal work sites and reference sites on which sediment removal had not been conducted for several years. At most sites, however, some vegetation shifts did occur. Most shifts were neutral or positive including: full or partial transition from one native-dominated vegetation type to another, disappearance of a non-native vegetation type, or increased total percent cover. Potentially negative changes occurred less frequently including: slightly increased invasive species cover, appearance or increase in amount of a non-native vegetation type, and decrease in total percent cover. There was no clear differentiation in the tendency for changes in vegetation dominance or quality to occur in work sites as compared to reference sites, with the exception of the initial reduction in erect emergent vegetation seen in certain non-tidal work sites. The study specifically focused on regrowth after sediment removal; however, routine vegetation management was ongoing during the course of the study.

No quantitative studies have been conducted on the effects of vegetation management on wetland or riparian vegetation. Anecdotal observations by District biological and vegetation management staff, however, indicate that the wetland extent and species composition are affected by vegetation management. Herbicide spraying likely reduces the amount of the target vegetation present (mostly cattails) in freshwater and tidal wetlands in years following the treatment. For example, in an herbicide-treated tidal reach of Sunnyvale East Channel, wetlands were still present in the years following regular spraying, but cattails were much less abundant than in an adjacent un-treated reach. A non-tidal reach of Saratoga Creek, which was also a sediment removal study site, experienced a marked reduction in cattail cover the year after herbicide spraying, but the amount of wetland slightly increased. By targeting erect emergent vegetation with herbicides, which kill the entire plant, other wetland vegetation types such as creeping emergent and non-native/annuals appear to be favored. In contrast, cattails that are removed by cutting re-sprout each year. Therefore, a reduction in abundance of erect emergent vegetation does not occur when hand removal is used. On the other hand, wetland vegetation is likely favored by the targeting of woody riparian saplings, either by herbicide or hand removal, that would otherwise shade out wetland plants.

3) Quantification of Impacts to Stream Vegetation

The projected impacts to in-stream vegetation are based on field surveys, calculations, and a special method for evaluating impacts from temporary but repetitive activities that was developed for this program. These factors are described below. Field surveys were primarily conducted in 1997 and 2000 to determine wetland extent in projected sediment removal areas (Rankin 1999a; Squires 1999; Rankin 1999b, TRA 2001). Wetlands were identified based on criteria set forth in the Corps of Engineers 1987 Wetland Delineation Manual (Environmental Laboratory 1987).

Freshwater wetland impacts from sediment removal were determined by conducting field surveys of randomly selected samples of channel segments within the major areas of projected impact. The results of the samples were extrapolated on a site-by-site basis to estimate the total impacts. Surveys were conducted during years of good growing conditions for wetland vegetation due to ample moisture and warm summer air temperatures. The surveys were conducted in late summer and early fall when in-stream freshwater wetlands in perennially wet locations are at their maximum extent.

Impacts to tidal wetlands were estimated in projected sediment removal work areas in 1997 using a different method. All proposed tidal sediment removal work areas were surveyed rather than sampled, as the total work areas in tidal reaches are much smaller than freshwater reaches. In each projected work location, the extent of wetland vegetation was measured directly or estimated in the field.

Areas of impact to stream vegetation from the vegetation management program were not measured in the field but were based primarily on records of the existing vegetation management program, which identify areas and type of target vegetation by stream reach (SCVWD 1999d). Herbicide spraying in the stream channel specifically targets either wetland or riparian vegetation (rather than broadcast spraying the entire channel bottom) depending on the design conditions of each channel reach. Therefore, each channel reach was identified as being subject to either removal of woody plants or aquatic plants, and this information was used to estimate the subsequent impacts to either riparian vegetation or wetlands, respectively. Therefore, no field surveys were necessary to estimate the amount of wetland and riparian vegetation potentially impacted by the vegetation management program. To classify vegetation management impacts, areas in which primarily wetland vegetation is targeted were categorized as wetland, and those in which primarily woody riparian vegetation is targeted were categorized as riparian, regardless of the predominant vegetation supported by the channel. For example, in some areas dominated by freshwater wetland vegetation, vegetation management only targets woody riparian vegetation. Such areas are categorized as riparian for the purposes of defining vegetation management impacts (Figure IV-B-13).

Projected vegetation management areas were refined to include the Pajaro River Basin areas where herbicides are not currently used, but are proposed for herbicide treatment as part of the program. For those areas, future herbicide use was projected based upon the area of existing hand removal and mowing operations and known target vegetation.

4) One-time Accounting Method for Stream Vegetation Impacts

A one-time accounting method for potentially significant impacts was developed for the program because impacts to stream vegetation from routine sediment removal and vegetation management are temporary but repetitive. The approach of this impact analysis is to count future impacts to any one section of creek one time only. Repetitive or overlapping stream maintenance activities in the same section of creek are not progressively added to the total impact acres.

The one-time accounting assessment method is relevant to assessing the impacts of the program because work is spread out over many years, routine maintenance takes place in only a portion of the total program work area in any given year, and stream vegetation regrows between cyclical maintenance events. This approach determines that a one-time assessment of impacts from routine maintenance activities adequately represents significant impacts of all future maintenance work in that same area, and the compensatory mitigation program is designed accordingly. For the program, permanent mitigation is proposed for these temporary, repetitive impacts.

In many stream sections, both sediment removal and aquatic herbicide application are undertaken, but in different years within the stream's particular maintenance cycle. For example, sediment removal may be conducted in year one. The following year, herbaceous wetland vegetation may begin to establish where the sediment was removed. In year three, vegetation may be sufficiently established to pose a potential flood hazard, so herbicide is applied to kill the targeted vegetation. Herbicide applications may continue in subsequent years. In the meantime, sediment accumulates until it eventually reaches a point where flood capacity is significantly reduced and sediment removal is again required.

In those sections of creek where both sediment removal and vegetation management activities are undertaken, sediment removal was designated as the primary effect and therefore used to project the future impacts. This approach was taken because sediment removal tends to affect all or most of the channel bottom, whereas herbicide treatment is more selective and affects a smaller area of the channel bottom. Likewise, only the first time that either sediment removal or herbicide treatment is conducted on a section of creek is counted as an impact, and repeat treatments at that same location in subsequent years are not counted as additional impacts. The projected impacts to in-stream wetland and riparian vegetation are provided in Table IV-B-7. The impact projections from vegetation management provided in Table IV-B-7 represent sections of creek where only channel vegetation management work is undertaken. Vegetation management impacts to stream vegetation appear relatively small compared to sediment removal because sediment removal numbers include the areas of overlap.

c. Determination of Wildlife and Fisheries Impacts

The District developed the impacts assessment for wildlife and fisheries using general life history and habitat requirements for each of the five vertebrate classes (e.g., fish, amphibians, reptiles, birds, and mammals), several invertebrate groups (e.g., mollusks and insects), and a cumulative grouping referred to as biodiversity (e.g., food web support, species richness, species composition). The impact analysis then looked at each of the four project components (sediment removal, vegetation management, bank protection, and minor activities) broken down by location (tidal, freshwater) and stream conditions (wet, dry). The District then evaluated how each of the major taxa and biodiversity components would be affected by these work components. The District then determined impact significance based upon the Thresholds of Significance described above. The detailed impact analysis by taxa, biodiversity, and work component (Padley 2001) is summarized in the impact evaluation below. This EIR provides a discussion of the impacts based upon the Significance Criteria.

Impacts to wildlife and fisheries from the SMP were systematically evaluated at both the project level and cumulatively. These impacts were first evaluated without the implementation of BMPs to identify which activities were potentially significant. The potentially significant impacts were then re-evaluated with the application of the program BMPs to determine if the implementation of BMPs would reduce the level of impact to less-than-significant. Those impacts that remained potentially significant even with BMP implementation were then re-evaluated with the implementation of the program's compensatory mitigation to determine if implementation of that mitigation would reduce the level of impact to less-than-significant. Impacts that remain significant even with implementation of BMPs and compensatory mitigation are described as significant and unavoidable.

The conclusions of this process are described below, with all impacts that were considered potentially significant without BMP implementation discussed first. This section concludes with a brief discussion of impacts determined to be less-than-significant. The code for the relevant significance criterion is provided in parenthesis.

Table IV-B-7. Summary of in-channel vegetation impacts in acres.

Work Activity	Stream Vegetation Impacts
	Freshwater Wetlands	Tidal Wetlands	Riparian Vegetation
Santa Clara Basin Streams
Sediment Removal	61	29	0
Vegetation Management	23	1	32
Santa Clara Basin Total	84	30	32
Pajaro River Basin Streams
Sediment Removal	19	0	0
Vegetation Management	6	0	46
Pajaro River Basin Total	25	0	46
SCVWD Streams Total	109	30	78
Canals
Sediment Removal	n/a	n/a	n/a
Vegetation Management	7	0	0
Canals Total	7	0	0
Total SMP	116	30	78

Source: SCVWD 3/01

Note: Impact projections from vegetation management represent sections of creek where only channel vegetation management work is undertaken.

d. Impacts Determined to be Potentially Significant

1) Impacts to Sensitive Plant Communities

Impact Bio-1: Sediment removal and vegetation management would impact in-stream wetland and riparian vegetation (Criterion Bio-1).

Implementation of the program would cause temporary but repetitive impacts to 116 acres of freshwater wetlands, 30 acres of tidal wetlands, and 78 acres of in-stream riparian vegetation due to sediment removal and vegetation management in stream channels. Concrete-lined channels are included in these projections as well as earthen channels. Seven of the 116 acres of freshwater wetlands occur in water delivery canals. Refer to Table B-IV-7 for a summary of vegetation impacts and Table II-4 for a breakdown of vegetation impacts by work activity type. Figure IV-B-13 shows the location of projected impacts to stream vegetation. As described in the introduction to the significance criteria for this chapter, any removal of wetland or riparian vegetation from sediment removal or vegetation management activities is considered cumulatively significant for the purposes of the SMP. These impact acres are based on the one-time accounting method described above and on the implementation of the following BMPs, which would reduce the impacts of removing wetland and in-stream riparian vegetation:

1.13	Prevent Scour Downstream of Sediment Removal
2.1	Minimize vegetation removal
3.6	Remove Sediment from One Side of Large Channels in Alternate Years

Implementation of the BMPs referenced above would reduce the adverse impacts of the SMP caused by removing wetland and in-stream riparian vegetation; however, the vegetation would be lost and residual impacts would remain. Implementation of the compensatory mitigation proposed for the SMP would reduce these residual impacts to tidal wetlands, freshwater wetlands, and instream riparian vegetation to a less than significant level. The effect of the compensatory mitigation on these three resources, as well as a summary of other related impacts, is described in the following discussion:

Tidal Wetlands

For tidal wetland impacts, no new tidal work areas are projected, and, in the Pajaro River Basin where the switch to herbicides is proposed, there are no tidal areas. Thus, the removal of 30 acres of tidal wetlands over the next 20 years would be a continuation of existing practices and adoption of the SMP would not result in any new adverse change in ongoing effects. The compensatory mitigation program includes restoration of 30 acres of tidal wetlands at a location either directly adjacent to or no farther than 7 miles from the tidal wetland impact areas. The restoration site is expected to support permanent tidal wetland similar to or of higher quality than the tidal wetland temporarily impacted by repetitive maintenance activities. Refer to the more extensive description of this mitigation measure in SMP Chapter 5. This mitigation measure is therefore considered sufficient to reduce the level of impacts to tidal wetlands to a less than significant level.

Freshwater Wetlands

For freshwater wetlands, sediment removal is projected to occur on approximately six miles of streams (five miles in the Santa Clara Basin and one mile in the Pajaro River Basin) that have not undergone regular maintenance in the past. Work in this area would affect three acres of freshwater wetlands in the Santa Clara Basin and none in the Pajaro River Basin. In the Pajaro River Basin, vegetation management is projected to occur on an additional 10 miles of streams where vegetation management has not been undertaken on a regular basis in the past, which would affect 4 acres of freshwater wetlands.Thus, the SMP would affect 116 acres of freshwater wetlands in the future, of which 7 acres would be a new adverse change.

The compensatory mitigation program includes creation of 14 acres of freshwater wetland (10 in the Santa Clara Basin and 4 in the Pajaro River Basin) and 920 to 1210 acres of stream and watershed protection to compensate for impacts to freshwater wetlands. The locations of these mitigation components will beallocated so that they occur within each basin at approximately the same level as the impacts. The freshwater wetland creation sites will occur at a few locations on the valley floor as compared to the impact areas, which are spread throughout each basin. Although the freshwater wetland creation sites will not be instream as are the impacted freshwater wetlands, they have an advantage of not being subjected to routine disturbance from flood protection maintenance as the impacted sites are, and they will provide habitat for common local wildlife and wetland-related plants in a streamside setting. The types of wetland plant species affected are widespread and regenerate quickly, thus it should not be difficult to create new wetlands of similar or higher quality.

The specific locations of the stream and watershed preservation efforts have not been chosen yet. They are generally expected to be farther up in the watershed than the impacts, however, since the upper watershed is where land suitable for preservation is most available. The type of stream habitat protected under the stream and watershed component is different than the instream freshwater wetland impacted in modified earthen and concrete channels, but the former consists of more structurally and functionally complex native riparian and riverine habitat that occur on less altered stream reaches.

Refer to the more extensive description of these mitigation measures in SMP Chapter 5. Because of the size and quality of the freshwater creation and stream and watershed compensation components, they are considered sufficient to reduce the level of impacts to freshwater wetlands to a less than significant level.

In-stream Riparian Vegetation

No new work areas are projected that would affect in-stream riparian vegetation. The additional impact to in-stream riparian vegetation from the conversion to herbicide use in the Pajaro River Basin is discussed under Impact Bio-6 below. Thus, the removal of 78 acres of in-stream riparian vegetation of a sapling size over the next 20 years would be a continuation of existing practices, and adoption of the SMP would not result in any new adverse change in ongoing effects.

The compensatory mitigation program includes control of 80 acres of giant reed over a 10-year period to mitigate for the impacts to riparian vegetation. This program includes associated efforts such as mapping, revegetation, monitoring, and education. Refer to the more extensive description of this mitigation measure in SMP Chapter 5. Since giant reed displaces open water and native riparian and wetland plant communities of freshwater streams, its control is appropriate compensation for impacts to sapling riparian vegetation caused by channel vegetation management activities. The giant reed control program will be spread throughout the county, as are the impacts, although control areas will be targeted to those locations where which the most habitat value can be obtained from sustained control efforts. The giant reed control program will reduce the impacts to riparian vegetation to a less than significant level.

An additional 45 acres of giant reed control is proposed to compensate for any lag time between maintenance impacts to stream vegetation and implementation of the tidal wetland restoration, freshwater wetland creation, and stream and watershed protection mitigation components.

Other Impacts

With the exception of a small amount of fill, which may occur from some bank protection projects, the SMP would not cause a loss of acreage of jurisdictional waters. Incidental fill is expected to be minimal due to the employment of BMPs. The direct effects to woody riparian vegetation from bank protection were not quantified. Bank protection rarely directly impacts woody riparian vegetation. Because bank protection effects on riparian vegetation primarily affect wildlife, this impact is discussed below in the Impacts to Wildlife Species section (see Impact Bio-5). The cumulative adverse impact of the loss of wetland and in-stream riparian vegetation on wildlife is also discussed in that section (see Impact Bio-4). The additional impact to freshwater wetlands from the conversion to herbicide use in the Pajaro River Basin is discussed below under Impact Bio-6.

Impact Bio-2: The project could result in removal of heritage-sized trees (Criterion Bio-3).

Heritage-sized trees (18" dbh) could be removed during maintenance. Although not common, such trees may be removed for installation of bank protection measures or may be removed for pre-emptive maintenance (e.g., a tree that poses a risk of falling). These large trees may provide valuable wildlife habitat, including raptor nesting sites, bat roosting sites, and foraging areas for birds. Trees that are in a state of decline and standing dead trees (snags) often provide some of the highest quality habitat due to holes, expanded crevices, and foraging quality, and even non-native trees of this size are valuable. Replacement of the values provided by such trees through regrowth takes decades. The loss of heritage-sized trees would be a significant impact. Implementation of the following BMPs would reduce this potential impact to a less than significant level:

2.1	Minimize vegetation removal
2.2	Minimize Stream Access Impacts
2.8	Replace heritage trees
3.9	Retain Woody Materials and Vegetation

Impact Bio-3: Program implementation could introduce invasive plant species into native, riparian, or wetland habitat areas (Criterion Bio-4).

Mowing and discing may create conditions suitable for additional spreading of invasive plant species such as yellow star thistle. District staff have observed yellow star thistle seedlings growing vigorously after grassy areas have been mowed. The areas where this effect is most likely to occur are earthen levee roads in the Pajaro River Basin. Such areas would be treated with selective spot treatment of herbicides under the SMP; thus; this effect would be reduced.

Bare upland soils left after construction of temporary access ways or installation of a bank protection site could encourage growth of weedy species, although the District has not observed this effect after sediment removal work in the channel bottom. Mulching or erosion control mixes could include and thus introduce invasive non-native species. Introducing invasive plant species could have a significant adverse effect on habitat. Implementation of the following BMPs would reduce this potential impact to a less than significant level:

2.1	Minimize vegetation removal
2.5	Planting
2.6	Mulching
2.7	Seeding

2) Impacts to Wildlife Species

Impact Bio-4: The cumulative impact of sediment removal and vegetation management would fragment wildlife habitat (Criterion Bio-5).

Fish, wildlife and plants live in habitat areas where conditions are suitable to carry out their life history functions. These patches of habitat not only must be large enough to support the individual but also must be in proximity of other individuals to support populations. Habitats along stream corridors are generally linear features on the landscape and may vary in width. Stream maintenance activities can alter these habitat patches by breaking them into smaller and disjunct pieces. This breaking apart of the habitat is known as fragmentation.

Fragmentation is considered to be detrimental to most fish and wildlife species. The problem with fragmentation is twofold; first, as habitat patches become smaller they are unable to support as many individuals (patch size); second, the area between habitat patches may be unsuitable for species to traverse from one habitat patch to another (connectivity). In extreme cases the habitat patches may become too small to support individuals or too isolated to support a species or its population.

Vegetation management and sediment removal can affect both patch size and connectivity when they remove vegetation over long reaches of creek, and change the vegetation structure and composition in a way that creates barriers to wildlife. By creating open areas, or patches with unsuitable vegetation types, these activities can restrict some wildlife species from moving between distant patches or even can temporarily eliminate a local population. For example, amphibians are affected by vegetation management in streams because this activity removes their cover to hide, and secondarily results in loss of invertebrates on which the amphibians forage. Sediment removal can change the local hydrology of a stream so that pools and still waters are replaced, at least temporarily, by runs which are not suitable for breeding. Amphibians have limited ability to move to another section of stream or another stream which are not being disturbed by maintenance in that particular annual cycle. Thus, some amphibians may be lost due to limited resources, and even if they do survive, they may not be able to travel to suitable locations to breed.

The cumulative effects of sediment removal and vegetation management on instream vegetation are described in the Impact Bio-1 above. That evaluation focuses on the impacts to vegetation, but since vegetation, in part, is the structure which provides wildlife habitat, it also indicates the level of fragmentation on wildlife. Common wildlife populations found in sites that are projected sediment removal and vegetation management work areas must be somewhat acclimated to these conditions since they are caused by a program of maintenance that is already ongoing in almost the entire work area. However, over a period of 20 years, separate populations of some wildlife species on different streams may not be able to recover or move between maintenance events, and a local population may be lost. These local losses may be significant when evaluated across the entire work area.

Mitigation:

Implementation of the following BMPs would reduce this impact:

1.13	Prevent Scour Downstream of Sediment Removal
2.1	Minimize vegetation removal
3.6	Remove Sediment from One Side of Large Channels in Alternate Years

Implementation of the BMPs referenced above would reduce the potential habitat fragmentation caused by sediment removal and vegetation management. Likewise, the compensatory mitigation program evaluated under Impact Bio-1 partially compensates for fragmentation effects. Cumulative adverse effects from fragmentation, however, may remain for those wildlife species that cannot easily move to undisturbed areas or the mitigation sites. Similar to the wetland regrowth study described in the Vegetation Responses to Impacts section above, the District has been studying the effects of sediment removal on birds. Results of this study are not known yet, so it is assumed that these effects are potentially significant.

The cumulative effect of fragmentation must also be viewed in the context of other activities. With increasing development in Santa Clara County, creeks are becoming the remaining refuge for some wildlife species. Over the next 20 years, the combination of continued stream maintenance and development of surrounding uplands, may result in some local wildlife populations dropping below a self-sustaining level on some creek sections.

Because the affected wildlife species occur in the very locations where flood protection must be maintained, the effects occur in many streams throughout the county, and some local populations may drop below a self-sustaining level which cannot be completely mitigated offsite, the fragmentation of wildlife habitat by stream maintenance activities over the next 20 years is considered an unavoidable and significant impact even with the implementation of the mitigation measures.

The effects of bank protection activities on fragmentation are described in Impact Bio-5.

Impact Bio-5: Bank protection would cause a loss of riparian vegetation functions and values, which would cause a significant cumulative adverse impact on wildlife and fisheries habitat (Criterion Bio-5, Criterion Bio-10).

Over the 20 year life of the program, some 20 miles out of the approximately 1,650 miles of bank (two sides of 825 miles of channel) under District jurisdiction can be expected to be modified for bank protection, and some increment of existing riparian vegetation can be expected to be lost. These cumulative losses would have a significant impact of wildlife. Because the riparian habitat provides valuable functions both in-stream and stream-side, and because these functions benefit fish and wildlife species, impacts to both fish and wildlife are discussed here. Other fisheries and aquatic impacts are addressed in the Impacts to Fisheries/Aquatic Habitat section that follows.

While no one has directly measured the decline in riparian forest on a consistent countywide basis, historic anecdotal information and known declines in bird faunas suggest that habitat quality has declined substantially. Many of the streams on which bank protection would occur have thus already been heavily impacted by numerous changes. Nonetheless, the narrow corridors (mostly <100 meters wide) of mature woodland that remain represent some of the most valuable riparian habitat in the San Francisco Bay Area (USACE 1986 cited in Rottenborn 1997).

Riparian corridors in Santa Clara County provide a wide range of biological functions. These functions range from providing habitat for fish and other aquatic species in the streams to foraging and nesting habitat for birds in the woodland canopy, to movement corridors for numerous terrestrial species. Even degraded riparian habitat provides significant habitat. Because any riparian habitats that are preserved usually provide the only patches of "natural" habitat remaining within urban areas, such areas may contribute to preserving wildlife population that could otherwise not persist in urban settings (Rottenborn 1997). Species potentially impacted by proposed bank protection measures include strictly aquatic species, such as fish, strictly terrestrial (upland) species, such as songbirds, and numerous species that move between the aquatic and adjacent upland habitat, such as frogs.

Even though the actual work at most bank protection work sites removes few, if any, mature riparian trees, the placement of additional hardscape within stretches of vegetated bank is a permanent change, and depending on the design, can eliminate the potential for future vegetation at these locations. The greater the number and/or size of gaps in what was once a continuous band of habitat, the more difficult for plants and animals to maintain healthy, stable populations within the habitat that is left. If gaps are large enough, recolonization of denuded or degraded areas along the banks by the native plant communities becomes more difficult and uncertain. The result may be the gradual disappearance of the riparian woodlands and their replacement with ruderal or exotic landscaping vegetation from neighboring uplands. Although bank protection with hard scape will not cause all these problems, it could contribute to the increasing fragmentation of the natural bank landscape along with other causes such as urbanization, downcutting, and subsidence of the groundwater table

The habitat fragmentation that is increased each time vegetated or potentially vegetated bank is replaced with hardscape material also impacts wildlife. Collectively, the total bank protection activities on a stream or reach of stream is a potentially significant impact on connectivity and may significantly affect patch size. In stream reaches where hardscape bank protection is necessary, the impacts would presumably be greater than where biotechnical techniques are used if it is in a location where habitat is present upstream or downstream of the site. Increasing the amount of hardscape along a channel reduces the amount of cover available to wildlife traversing these reaches and may make them vulnerable to predation. In some cases the wildlife will not even try to cross open habitat areas.

For example, in a study on chaparral habitat in Southern California, Soule (in Diamond 1988) found that habitat areas cut off from each other by 50-100 meters of development was enough to effectively isolate some bird species. Soule suggested that strips as small as 1-10 meters may be enough to provide an effective corridor for sedentary birds (in Diamond 1988). Some species can cross bare areas or areas of unsuitable habitat, but this movement exposes them to additional mortality by either predation or desiccation. The degree of impact depends upon the species and the length of bare habitat temporarily created by the project. Species that are susceptible to increased predation from loss of cover include many neotropical migrant bird species, amphibians, reptiles, and small mammals. Increased nest predation by corvids (crows, scrub jays), and mammalian predators has been correlated with reduction in habitat patch size and a decrease in density of vegetation at nest height. Habitat specialists such as warblers are the species most adversely affected by habitat reduction.

The loss of riparian habitat and its replacement with ruderal vegetation also contributes to the spread of opportunistic urban pest animal species at the expense of the species which are dependent upon native habitats. Opportunistic animals that co-exist well with humans and in altered landscapes include rats, raccoons, and red fox. These species are often not native to these areas and out-compete and prey on the more sensitive species. For example, red fox predation on eggs and young is thought to be a major factor in continuing clapper rail decline in the Bay Area.

Riparian vegetation and streambanks that would be impacted by bank protection, also provide important in-stream functions. Bank protection would remove undercut banks, woody debris, and other forms of escape cover for fish and other aquatic organisms. It could eliminate nesting sites in banks for kingfishers. Removal of trees and shrubs on upper banks and along the streambed during bank protection work would remove shade and overhanging branches that provide escape cover and food sources. Impacts of loss of shade would be greatest in habitats where water temperatures are presently marginal for salmonid spawning or rearing, primarily in habitat categories 3 (mixed native; spawning) and 5 (potential trout habitat).

These stream functions potentially affected by bank protection can be classified as either in-stream functions primarily affecting the aquatic environment or stream side functions primarily affecting the riparian environment, but also affecting the aquatic environment. (Note that bank protection impacts that are specific to special-status species are discussed in the Impacts to Special-status Species section.) The following discussion oversimplifies the aquatic species habitat relationship, but is a reasonable guide for application of the programmatic mitigation included in the SMP for impacts to riparian functions and values from bank protection (see SMP Appendix E).

In-stream

In-stream functions provided in or immediately adjacent to the normal flow channel directly serve aquatic and semi-aquatic species. For the programmatic mitigation, the channel is defined to be the area below Ordinary High Water. Functions include:

• In stream Escape Cover: provided by undercut banks, large boulders, tree roots, downed trees, and other structural elements (including deteriorating bank protection projects)
• Hydraulic Complexity: resulting from the interaction of current with the same structural elements providing instream escape cover
• High Velocity Refuge: also provided by structural elements

Stream-side

The stream-side environment supports riparian vegetation and the functions riparian vegetation provides. Riparian vegetation benefits terrestrial species, as well as semi-aquatic amphibians and reptiles and fish. Functions include:

• Sediment stabilization: provided by riparian trees, shrubs, and grasses
• Shading and water temperature moderation: provided by mature riparian shrubs and trees
• Overhanging escape cover: provided by shrubs and grasses near the stream edge
• Coarse particulate organic matter (allochthonnes): organic material dropping into the stream in the form of leaves, insects, etc., that provide input for aquatic food webs
• Bird breeding and foraging habitat: provided by mature native riparian species, such as cottonwoods and willows, oaks, other trees, shrubs, forbs, grasses, and the streambank itself
• Foraging, refugia, estivation, and breeding habitat for semi-aquatic amphibian and reptile species: provided by low vegetation, rocks, downed materials, and the streambanks itself
• Foraging, breeding, hibernacula, and dispersal habitat for mammals: provided by the riparian vegetation and the streambanks substrate

The cumulative loss of these functions and reduction in their value would result in a significant impact.

Mitigation:

The following BMPs would reduce these impacts:

2.1	Minimize vegetation removal
2.3	Minimize Hardscape in Bank Protection Design
3.5	Minimize Loss of Aquatic Habitat from Bank Protection work
3.14	Maintain or Provide Escape Cover

Implementation of the BMPs referenced above would reduce the adverse impacts of hardscape installation for bank protection; however, over the life of the program habitat would be lost or reduced in value resulting in residual impacts. However, as stated in the Project Description (Chapter  II), the District has committed to installing no more than 50% of future bank protection projects under the SMP using hardscape methods. Although these residual impacts may be considered insignificant when reviewed on an individual site basis, when evaluated on a program basis the potential for significant, cumulative impacts remains. Implementation of BMP 3.5, for example, would replace functions and values lost via the mitigation provided in the Programmatic Impact Assessment and Mitigation for Routine Bank Protection Activities (SMP Appendix E), but that mitigation would not always occur at the impact site and therefore could result in a cumulative fragmentation effect. The cumulative impact from bank protection would thus remain significant and unavoidable.

Impact Bio-6: The cumulative effects of resuming herbicide use in the Pajaro River Basin would substantially reduce the value of the habitat for wildlife (Criterion Bio-5).

Currently, the District manually controls vegetation in the Pajaro River Basin. When the work is done in late summer or fall, as has been the practice for non-chemical control, the plants are able to resprout by the following spring and provide habitat for a few months during the summer before they are cut again. Under the SMP, however, glyphosate herbicides (e.g., Roundup and Aquamaster) would be used in the Pajaro River Basin on an estimated 57 acres of in-channel vegetation and 157 acres of upland vegetation adjacent to the channels. Unlike many mechanical control methods, the glyphosate herbicides kill the entire plant, including the roots. Species such as willows that might quickly resprout after mechanical control are instead killed entirely by herbicide application.

Even young willows have some habitat value. For example, yellow warblers, Wilson's warblers, and Pacific slope flycatchers will use young willows for shelter and feeding during migration, although they need mature willows for nesting. Although herbicides would not be applied to in-channel woody vegetation that is 2" dbh, willows frequently branch from the base and thus are below the spray threshold. Some of these willow clumps are likely well enough developed as to provide suitable nesting habitat for some species. Herbicide application would keep these willows and other woody and herbaceous vegetation in and along the channels at a very early growth stage.

Herbicide application would also likely reduce the overall extent of vegetation in the basin. The District estimates, for example, that if herbicide use resumes, the extent of in-channel vegetation in the basin that would be treated would be reduced over a period of several years. Many of these areas overlap with sediment removal areas; thus, according to the one-time accounting method developed for this program, the effects of the more effective herbicide application does not result in additional impacts to stream vegetation. However, for those areas in which vegetation management, but no sediment removal, is proposed, it is estimated that an additional two acres of freshwater wetland and one acre of riparian vegetation would be removed due to the efficiency of the herbicide treatment. An additional 3 acres have been included in the impact acres for freshwater wetland and riparian vegetation to compensate for this effect.

On the other hand, it is also possible that a switch to herbicides to control vegetation may not result in an overall loss of wetland vegetation but may shift the species composition in the basin by favoring species that are able to quickly regrow after application. District biologists observed that recent herbicide spraying on Saratoga Creek resulted in a shift of wetland vegetation type from cattails to creeping emergents; however, one year later, there was as much area of wetland vegetation as before. In some places weedy, invasive species may be favored as the denser overstory is removed, although this was not observed as an effect of sediment removal in the regrowth study and its potential for resulting from the use of a switch to herbicides is not known.

A change in the character of the vegetation in and along the channels could reduce shade, cover, and foraging and nesting habitat. The District proposes herbicide application on 24% (56 miles out of 241 miles of streams in the Pajaro River Basin within the District's jurisdiction) of the lowland streams in the Pajaro River Basin. Because this change would affect such a large area of vegetation and thus represent a significant local loss of the resources provided by this vegetation, this impact would be considered significant.

Mitigation:

The following BMPs would reduce the impacts of resuming herbicide use in the Pajaro River Basin:

2.1	Minimize vegetation removal
3.2	Minimize Impacts to Breeding Birds Via Site Assessments and Avoidance Measures
3.18	Herbicide Use in Aquatic Areas
3.19	Develop a Biodiversity Monitoring Program

Implementation of the BMPs referenced above would reduce the adverse impacts of resuming herbicide use in the basin; however, vegetation would be held to an earlier successional stage and the overall extent of the vegetation may be reduced or the species composition may change over time. Residual impacts would thus remain. Although these residual impacts may be considered insignificant when reviewed on an individual project basis, when evaluated on a program basis, the potential exists for significant, cumulative impacts by resuming herbicide spraying on 56 miles of streams in the Pajaro River Basin. The compensatory mitigation components Freshwater Wetland Creation, Stream and Watershed Protection, and Giant Reed Control would all aid riparian and freshwater habitat values. Since the amount of vegetation loss or conversion that may occur as a result of the resumed herbicide use is uncertain, and this may have a secondary effect of fragmentation to wildlife as described above, the cumulative impact would thus remain significant and unavoidable.

Impact Bio-7: Chemical use by the District, especially for rodent control, could adversely affect non-target species (Criterion Bio-5, Criterion Bio-12, Criterion Bio-13).

Ground squirrels and to a lesser degree, gophers, create underground burrows, which can threaten the integrity of levees meant to contain flood water or convey canal water. The burrows can allow water under pressure to pipe through the earthen barrier, increasing in flow and causing a localized, abrupt failure.

The District controls rodent damage in selected channels and canals by rodenticides applied by a contractor. Approximately 48 miles of channel is treated in the Santa Clara Basin and 30 miles of channel are treated in the Pajaro Basin. Nearly all of the canals are monitored and treated, when necessary. The contractor selects the method for treatment from those permissible by law and the County Agricultural Commissioner.

Currently, the majority of ground squirrel control is by a grain bait treated with chlorophacinone. In the year 2000, 1725 pounds of 0.01% bait was applied. The bait is scattered near the burrows and is attractive to rodents. In principal, non-target animals such as domestic pets and wildlife are not able to ingest much of the bait, or, in the case of birds, are not very susceptible to the poison. Animals that forage extensively for seeds, such as western harvest mice (Reithrodontomys megalotis), would be affected. US EPA registration warns of wildlife hazard. (See SMP Appendix H for a detailed discussion of rodenticide effects on wildlife).

Chlorophacinone is highly toxic to rodents and hence results in a quick kill; this reduces the tendency to secondary poisoning where partially intoxicated animals are taken as prey because target animals usually die in their burrows where bait is ingested (B. Hosea, pers. comm.). While this rodenticide seems to have a far lower potential for food chain effects compared with other rodenticides (e.g., Compound 1080), an unknown potential effect remains. Rodent control has the potential to eliminate or substantially reduce local small mammal populations.

Gophers are controlled by depositing strychnine treated bait in burrows underground. Many reptile and amphibian species use such burrows for estivation or as refugia. Most such species would be unlikely to consume treated grain.

In the past, fumigants have been used; these are placed down an actively used ground squirrel burrow and the burrow plugged with newspaper to allow moisture to generate highly toxic phosphine gas. While not affecting areas outside of direct treatment, there is the potential that the burrow is occupied by non-target animals such as amphibians and burrowing owls (B. Hosea, pers. comm.; see the discussion under Special-status Species, below). Secondary toxicity from zinc phosphide to mammalian predators (animals eating other animals that were exposed to the compound) is rather low, primarily because the compound does not significantly accumulate in the muscles of target species (B. Hosea, pers. comm.; see also SMP Appendix H). Studies have focused on the following predators: coyote, fox, mink, weasel, and birds of prey. Some of the toxic effects to predators have been due to the ingestion of zinc phosphide that was in the digestive tract of the target organism, but most of the toxic effects to non-target wildlife are due to direct exposures resulting from misuse or misapplication of this rodenticide.

Although herbicide spray is carefully limited to target vegetation, the spray may directly contact the skin of amphibians. The long-term effects of such exposure on amphibians is unknown, but due to the permeable nature of their skin, amphibians may be particularly susceptible to environmental toxins. Likewise, the local effects of herbicide use on invertebrates in not known.

It is difficult to assess the magnitude of the impacts of herbicides and rodenticides on non-target wildlife, but the potential exists for these impacts to be significant.

Mitigation:

Implementation of the following BMPs would reduce this potential impact to a less than significant level:

2.1	Minimize vegetation removal
3.1	Minimize Impacts to Special-status Animals Via Site Assessments and Avoidance Measures
3.18	Herbicide Use in Aquatic Areas
3.20	Minimize Herbicide Impacts on Non-target Species
3.21	Minimize Rodent Control Impacts on Non-target Species
4.7	Herbicide Use Requirements

Impact Bio-8: Maintenance activities could introduce invasive wildlife species (Criterion Bio-7).

Without implementing proper procedures, mitten crabs could inadvertently be relocated from the Santa Clara Basin into the Pajaro River Basin. The spread of mitten crabs into areas currently unoccupied by this invasive, non-native species would be a significant impact.

Mitigation:

Implementation of the following BMPs would reduce this potential impact to a less than significant level:

3.4	Mitten Crab Control Measures

Impact Bio-9: Maintenance activities could directly harm nesting species protected under the Migratory Bird Treaty Act and other statutes (Criterion Bio-8).

Migratory birds are protected under the Migratory Bird Treaty Act, and raptors (birds of prey) and their young are also protected under the Fish and Game Code. Covered species breed throughout areas of District jurisdiction. For example, belted kingfishers and swallows breed in streambanks, Bullock's orioles breed in riparian vegetation, horned larks breed in grasslands adjacent to channels, and raptors use trees along streams and at the edges of open fields for roosting and nesting. Native and non-native (e.g., Eucalyptus) species are used. Maintenance activities adjacent to nesting migratory birds could cause nest abandonment or the loss of young. Sediment removal or discing, mowing, or other vegetation management could cause the direct loss of nest. Additionally, woody debris on the banks such as standing dead trees (snags) are important nest and perch sites for many birds. Trees in "imminent danger" of falling are also subject to removal for maintenance. Such trees may also have active nests. The loss of active nests, eggs, or young would be a significant impact.

Mitigation:

Implementation of the following BMPs would reduce this potential impact to a less than significant level:

2.1	Minimize vegetation removal
3.2	Minimize Impacts to Breeding Birds Via Site Assessments and Avoidance Measures
3.9	Retain Woody Materials and Vegetation
3.19	Develop a Biodiversity Monitoring Program

4) Impacts to Fisheries/Aquatic Habitat

Impact Bio-10: Maintenance work conducted in channels could substantially interfere with migration, spawning, incubating, or rearing habitat for native aquatic species (Criterion Bio-10).

The cumulative adverse effects of bank protection on riparian vegetation functions and values have previously been described as significant and unavoidable (see above). Other impacts to fisheries could occur under the SMP that would be significant in the absence of BMPs. These effects are discussed here.

Much of the maintenance work conducted under the SMP requires that work be conducted in stream channels. Since work is generally not conducted in a live channel to avoid turbidity and other problems, the work site may have to be dewatered. Dewatering a stream could strand or even kill aquatic species and block fish movements. The residual effects of maintenance on in-stream habitat could also adversely impact aquatic species.

The persistence of many resident fish species within District streams in the face of the impacts of controlled releases, water diversions, and impediments to fish passage has been possible only because many of the species have very high rates of reproduction and so can recolonize depleted reaches when the opportunities are presented. Loss of spawning habitat in a particular reach of creek due to project activities can deplete that reach of fish hatchlings and juvenile fish that would ordinarily move downstream and recolonize other habitats that might have been depleted of fish.

Additionally, loss of woody debris can adversely affect aquatic species. Woody debris includes broken branches and entire trees that are snapped off or uprooted during high flows or by wind. Routine maintenance includes removal of woody debris along banks or in the channel bottom to reduce flooding potential. Woody debris in streams is important as cover for fish and as a nursery area for invertebrates such as aquatic insects that serve as food for the fish. These impacts would be significant.

Mitigation:

Implementation of the following BMPs would reduce these effects to a less than significant level.

2.2	Minimize Stream Access Impacts
3.7	Salvage Native Aquatic Vertebrates from Dewatered Channels
3.9	Retain Woody Materials and Vegetation
3.11	Avoid Dewatering an Entire Isolated Stream Reach
3.12	Maintain Low-flow Fish Passage
3.13	Remove Temporary Fills as Appropriate
3.14	Maintain or Provide Escape Cover
3.15	Restore Riffle and Pool Configuration of Channel Bottom
3.16	Restore Spawning Gravels in Work Site Areas
3.17	Reuse Sediments and Gravels As Appropriate

Impact Bio-11: Temporarily suspended sediment can adversely affect aquatic or semi-aquatic species (Criterion Bio-11).

Removing sediment or operating equipment in live streams is likely to stir up sediment and produce turbid streamflow. Additionally, vegetation removal would also lead to turbidity because the in-stream vegetation traps and holds sediments. Leaving bare soils that have been exposed during maintenance work unprotected could also lead to erosion into a stream. Suspended sediment in the stream is detrimental to aquatic life because it blocks fish gills, pores, and breathing structures. As the sediment drops out, it smothers bottom vegetation and invertebrates and covers gravels, some of which may be used for spawning.

Suspended sediment is a frequent condition of Santa Clara County streams during the winter months when high storm flows cause bank erosion and move large loads of accumulated sediment from upstream to downstream areas. During low flow periods such as when the sediment removal takes place, the sediment has dropped out and the clarity of the water is much greater, whether the source of flow in a stream is reservoir releases or seepage from groundwater. The appearance of sediment in the water during these low flow periods is an unusual environmental stress for the species dependent upon the dry season flow.

High turbidity levels could clog gills and eliminate sensitive fish and aquatic insect species. If not retained on site, the sediment could adversely impact stream substrate conditions downstream reducing aquatic insect abundance or quality of gravels for fish spawning. These impacts would be significant.

Mitigation:

Implementation of the following BMPs would reduce these effects to a less than significant level:

1.1	Conduct Work During Low Flow Periods
1.2	Tidal Work Areas
1.3	Dewater/ Bypass Water at Non-tidal Sites
1.4	Avoid Erosion When Restoring Flows
1.5	Erosion and Sediment Control Measures
1.6	Use of Wheel and Track Mounted Vehicles in Stream Bottoms
1.7	Pump/ Generator Set Operations and Maintenance
1.8	Handle Sediments So As to Minimize Water Quality Impacts
1.9	Soil Stockpiles
1.12	Groundwater Management
1.14	Minimize Sediment Transport Downstream from In-channel Herbicide Sites
1.15	Prevent Erosion Downstream of Bank Protection Sites
2.2	Minimize Stream Access Impacts
3.10	Conduct In-Channel Work During the Dry Season

e. Impacts to Special-status Species

The analysis for impacts to special-status species was prepared by EDAW biologists. In general, when evaluating impacts to listed species, any loss in the number of individuals or occupied habitat was considered significant. Impacts to unoccupied habitat that was otherwise suitable for listed species was only considered significant if it was likely to become occupied over the 20-year life of the SMP. For other special-status species, impacts were determined to be significant only if they substantially reduce the availability of suitable habitat or cause a significant reduction to the local or regional population.

All three major types of stream maintenance activities have the potential to affect special-status species. Minor stream maintenance activities (e.g., grading existing access roads, levees, and rodent control) also could cause impacts to some special-status species. Loss or disturbance of habitat would be the most common impact anticipated, but some stream maintenance activities could also result in the loss of individuals. Short-term impacts would include temporary disturbance to individuals or habitat loss. Long-term impacts would include repeated disturbance, which would preclude individuals from occupying a work area throughout the 20-year life of the SMP or permanent habitat alteration.

Habitat-based Groupings of Special-status Species

Stream maintenance activities are expected to have similar impacts on species that have similar habitat requirements. Therefore, species that could be significantly affected by maintenance activities have been grouped into the following habitat-based categories. These categories have been developed for the purpose of this impact analysis because most BMPs are designed to minimize impacts at the habitat level rather than at the species level. Although impacts to special-status species are discussed under group headings, it is important to note that each species within a group was evaluated separately when determining whether or not significant impacts were anticipated.

• Group A Semi-aquatic reptiles and amphibians: California red-legged frog, foothill yellow-legged frog, western pond turtle, and San Francisco garter snake

• Group B Anadromous salmonid fish: steelhead (South/Central California ESU and Central California ESU) and chinook salmon
• Group C Birds that are dependent on riparian or marsh habitat: western least bittern, least Bell's vireo, yellow warbler, and tricolored blackbird
• Group D Plants, birds, and mammals that are dependent on salt and tidal wetlands: California sea-blite, California black rail, California clapper rail, saltmarsh wandering shrew, saltmarsh harvest mouse, saltmarsh common yellowthroat, and Alameda song sparrow
• Group E Raptors that nest in woodland habitats: Cooper's hawk, white-tailed kite, golden eagle, and long-eared owl
• Group F Invertebrates that are associated with serpentine habitat: Opler's longhorn moth and bay checkerspot butterfly
• Group G Shorebirds that use salt pans and levees: western snowy plover
• Group H Animals that occupy grasslands and other open habitats: California horned lizard, northern harrier, burrowing owl, loggerhead shrike, and California horned lark
• Group I Upland and riparian plants: Tiburon paintbrush, coyote ceanothus, pappose spikeweed, Mt. Hamilton thistle, clustered lady's slipper, western leatherwood, Santa Clara Valley dudleya, San Francisco wallflower, smooth lessingia, Metcalf Canyon jewelflower, most beautiful jewelflower, Franciscan onion, Santa Cruz manzanita, big-scale balsamroot, Santa Clara red-ribbons, San Francisco collinsia, Hospital Canyon larkspur, fragrant fritillary, Loma Prieta hoita, arcuate bush mallow, Hall's bush mallow, rayless ragwort, maple-leaved checkerbloon, and saline clover

Best Management Practices Incorporated into the SMP

The BMPs that are applicable to special-status species are listed in the following table. The BMP identity codes are included in the text discussion where applicable.

1.14	Minimize Sediment Transport Downstream from In-channel Herbicide Sites
1.15	Prevent Erosion Downstream of Bank Protection Sites
1.3	Dewater/ Bypass Water at Non-tidal Sites
1.4	Avoid Erosion When Restoring Flows
1.5	Erosion and Sediment Control Measures
2.1	Minimize vegetation removal
2.2	Minimize Stream Access Impacts
2.3	Minimize Hardscape in Bank Protection Design
2.5	Planting
2.6	Mulching
2.7	Seeding
3.1	Minimize Impacts to Special-status Animals Via Site Assessments and Avoidance Measures
3.2	Minimize Impacts to Breeding Birds Via Site Assessments and Avoidance Measures
3.3	Avoid serpentine habitat
3.6	Remove Sediment from One Side of Large Channels in Alternate Years
3.7	Salvage Native Aquatic Vertebrates from Dewatered Channels
3.9	Retain Woody Materials and Vegetation
3.10	Conduct In-Channel Work During the Dry Season
3.11	Avoid Dewatering an Entire Isolated Stream Reach
3.12	Maintain Low-flow Fish Passage
3.15	Restore Riffle and Pool Configuration of Channel Bottom
3.16	Restore Spawning Gravels in Work Site Areas
3.19	Develop a Biodiversity Monitoring Program
3.18	Herbicide Use in Aquatic Areas
3.20	Minimize Adverse Effects of Herbicides on Non-target Species
4.5	Vehicle and Equipment Cleaning
4.7	Herbicide Use Requirements
6.1	Spill Prevention
6.4	Vehicle and Equipment Fueling
6.5	Vehicle and Equipment Maintenance

Impact Bio-12: Sediment Removal would adversely affect special-status species.

Group A (semi-aquatic reptiles and amphibians)

Group A species are found in freshwater habitat and adjacent riparian and upland vegetation throughout the year. Sediment removal projects are proposed in habitat that is suitable for these species. These projects could result in the loss of individuals as well as suitable habitat for the following species in Group A: California red-legged frog, foothill yellow-legged frog, western pond turtle, and San Francisco garter snake. At least 6 known California red-legged frog sites will be impacted by the SMP. An unknown amount of western pond turtles may be impacted by the SMP.

To avoid injury or destruction of individuals or egg masses, suitable habitat will be surveyed and avoidance measures would be implemented prior to the start of sediment removal projects (BMPs 3.1 and 3.7). Project-specific resource protection measures, such as set-backs or buffer zones, will be employed to the maximum extent practical to minimize impacts to occupied habitat. Restoring the riffle and pool configuration of the channel bottom (BMP 3.15) after sediment removal will minimize permanent habitat alteration. Avoiding dewatering all of an isolated reach of a creek (BMP 3.11) and removing sediment from one side of the channel in alternate years (BMP 3.6) may reduce the likelihood that individuals will be injured or destroyed by sediment removal activities.