PUBLIC REVIEW DRAFT
NORTH COAST RAILROAD 
SOUTH END ALTERNATE PROJECT 
PROGRAMMATIC ENVIRONMENTAL ASSESSMENT





Prepared for
Federal Emergency Management Agency
Region IX
1111 Broadway, Suite 1200
Oakland, California 94607-4052

November 2003


Prepared by


Nationwide Infrastructure Support Technical Assistance Consultants
A Joint Venture of URS Group, Inc., and Dewberry & Davis LLC
500 12th Street, Suite 200
Oakland, California 94607
Contract No. EMW-97-CO-0173

Task Order #61

DRAFT Programmatic Environmental Assessment
FEMA-1203-DR-CA
Federal Emergency Management Agency, Region IX


Project Name:	South End Railroad Project
Subgrantee: North Coast Railroad Authority		
PA ID #: 000-91024	
Date: November 2003
Project Location: Russian River Division of the North Coast Railroad Authority, from Lombard in Napa County (MP 1) to Willits in Mendocino County (MP 142.5)
	

1.0	INTRODUCTION

The North Coast Railroad Authority (NCRA) has requested funding from the Federal Emergency Management Agency (FEMA) through the California Governors Office of Emergency Services (OES) for repairs and modifications to the southern portion of the Northwestern Pacific Railroad (NWP) (South End Railroad Project or project).  The study area for this project extends from Willits in Mendocino County (MP 142.5) south to Lombard in Napa County (MP 1) and constitutes NCRAs Russian River Division (Figure 1).  

The NWP, including the South End portion, is not currently operational.  NCRA has identified a series of actions (described in Section 2.2 of this document as the Proposed Action Alternative and also listed in Appendix A) that would restore the railroad infrastructure and, in conjunction with other actions to be taken by NCRA, contribute to the eventual restoration of independent freight operations along the South End of the railroad corridor.  FEMA would provide Public Assistance Program funding through OES for the identified actions.

Since the exact scope, location, and time frame for individual actions to be undertaken for the South End Railroad project are currently undefined, FEMA has prepared this Programmatic Environmental Assessment (referred to herein as the South End Railroad PEA).  The South End Railroad PEA has been prepared pursuant to:

* The National Environmental Policy Act (NEPA);

* The Council on Environmental Qualitys regulations implementing NEPA (40 Code of Federal Regulations [CFR] Parts 1500-1508); and 

* FEMAs implementing regulations (44 CFR Part 10).

The South End Railroad PEA evaluates general environmental effects of the Proposed Action and provides the framework for additional evaluation under NEPA for specific actions, as appropriate.  When a specific action within the Proposed Action is ready for decision, FEMA will have an opportunity to review the action in conjunction with the South End Railroad PEA to determine if more site-specific analysis and documentation would be required at that time.  If the level of analysis provided by the South End Railroad PEA is insufficient for the specific action, then additional analysis would be tiered from this PEA, in accordance with 40 CFR Part 1508.28.

1.1	Background
  
The NWP, which began operation in 1907, extends approximately 317 miles from Arcata in Humboldt County to Lombard/Napa Junction in Napa County.  In 1984, ownership of the NWP was split between two organizations at Willits in Mendocino County.  The Southern Pacific Railroad operated the southern half of the railroad, while the northern portion was sold to the Eureka Southern Railroad.  Between 1984 and 1996, the two portions of the NWP were operated independently.

NCRA was formed in 1989 by the California Legislature under the North Coast Railroad Authority Act to ensure continuation of railroad service in northwestern California.  In 1992, the state purchased the railroad line from Willits north to Arcata.  A separate transaction in 1995 added the railroad line between Healdsburg and Willits to NCRA's holdings.  NCRA, the Golden Gate Bridge, Highway, and Transportation District (Bridge District), and Marin County set up a joint powers authority called the Northwestern Pacific Railroad Authority (NWPRA).  This public-private partnership took over the ownership of rail facilities and tracks along the southern portion of the NWP from Healdsburg south through Schellville in Sonoma County, where the railroad then feeds a 12-mile short-line through Napa County that ultimately connects to the Union Pacific mainline at Fairfield-Suisun in Solano County.  Freight service and related maintenance of this portion of the railroad became the responsibility of NCRA under an agreement with NWPRA.  Until 1998, freight service operated twice daily along the railroad, carrying mainly natural resource products.  Although it was chartered by a state mandate, NCRA was not funded by the state. 

The railroad became inoperable as a result of damage sustained during the winter storms of 1997-1998.  The President declared a disaster (FEMA-1203-DR-CA) for the counties through which the railroad passes.  Consequently, NCRA applied through OES to FEMA for funding under the Public Assistance Program to restore the pre-disaster operations of the railroad.  Because only disaster-related portions of the proposed repairs were eligible for Public Assistance funding, NCRA was to be responsible for repairing sections of the track that were unstable or in deferred maintenance before the disaster. 

Given the substantial differences in the magnitude and nature of repairs required for the two sections of the railroad (north and south of Willits, respectively), and in consideration of the independent utility of the respective sections, FEMA evaluated the environmental effects of the proposed repairs for the sections separately.  Only minor repairs were anticipated for the southern section of the railroad; therefore, FEMA determined that these repairs were categorically excluded from further review under NEPA, pursuant to 44CFR 10.8 (d)(2)(xvi).  FEMA determined that an Environmental Assessment (EA) for the northern section was required.  FEMA completed a draft of the EA in 2000.

Once NCRA completed disaster-related repairs to the southern section, commercial freight service resumed between Lombard and Penngrove in January 2001.  However, service was discontinued in September 2001 due to lack of funds for operation and completion of further rehabilitation work.  Subsequently, NCRA identified additional maintenance and infrastructure improvements that would be necessary to restore service in the southern portion of the NWP.  Meanwhile, the rehabilitation of the northern section of the railroad continued to be delayed.  In June2003, NCRA requested through OES that FEMA approve a transfer of the Public Assistance funds intended for the northern railroad project to an alternate project.  The alternate project would involve necessary actions, combined with other activities to be undertaken separately by NCRA, for the rehabilitation of the southern portion of the NWP so that it could function as an independently operated freight railroad.  NCRAs letter describing the alternate project is provided in Appendix A.

1.2	Concurrent Projects in the Vicinity

1.2.1 	SMART Commuter Rail Project

In 1998, the Sonoma-Marin Rail Transit Commission (SMART Commission) was established as a ten-member commission of county and city government representatives from Sonoma and Marin counties.  The SMART Commission was charged with developing a 75-mile commuter rail service between Cloverdale in Sonoma County to a San Francisco-bound ferry terminal in Marin County.  Technical and environmental studies are currently underway for the proposed passenger rail service with plans for up to 14 stations along its route.  Based on the proposed commuter route plans, the SMART project would share approximately 60 miles of track with NWPRA, over which NCRA maintains an exclusive freight easement.  Maintenance and operations of tracks shared for commuter, freight, or excursion services would be coordinated through operating agreements.

In 2002, California Assembly Bill 2224 (AB 2224) created a new entity, the Sonoma Marin Area Rail Transit District (SMART II). The new rail district, which became effective on January 1, 2003, consolidated the SMART Commission, NWPRA, and the Bridge Districts authority and assets owned by those bodies into a single rail district. The new SMART District has inherited the former SMART Commissions work of developing a commuter rail system and placing funding initiatives before district voters to help fund implementation and operation of the transit system.  AB 2224 also transfers NWPRA assets to the new district.  As such, tracks and rail facilities over which NCRA plans to operate freight service through the South End Railroad Project are also owned by the new SMART II rail district.  Under the transfer, however, NCRA continues to have an exclusive freight easement over the South End Railroad Project right-of-way.  As freight service along the corridor is expected to resume before passenger service is scheduled to begin, operating agreements between NCRA and the new SMART district will govern the eventual coordination of operations. 

 
1.2.2 NCRA Northern End Reopening Project

As noted in Section 1.1 above, repairs to the northern portion of the NWP are being undertaken separately by NCRA.  Although the timing of the project implementation is not certain at this time, the project may contribute to cumulative effects in the area.  These effects are discussed in Section 4.0.
1.3	Scope of Document
The South End Railroad PEA tiers from the Final Programmatic Environmental Assessment for Typical Recurring Actions Resulting from Flood Disasters in California (Flood PEA) (FEMA 1998) and hereby incorporates the Flood PEA by reference, in accordance with 40 CFR Part 1508.28.  The Flood PEA can be accessed through FEMAs website at www.fema.gov/regions/ix/env/nhpapa.shtm.  

The Flood PEA covers, in broad terms, the actions and alternatives described in this document. The South End Railroad PEA further describes the effects of certain categories of actions associated with the rehabilitation of the railroad line between Willits and Lombard (as described in Appendix A).  However, as specific actions are identified, additional environmental review may be warranted.  
This document describes the potential environmental impacts of undertaking the proposed actions collectively referred to as the South End Railroad Project (defined in Appendix A).  These are actions toward which FEMA funds may be applied under the purview of the alternate project.  This document also evaluates impacts that may result from maintaining status quo and leaving the railroad in its current state (No Action Alternative).  FEMA anticipates that this South End Railroad Project PEA will ensure compliance with NEPA for most of the proposed actions under this project, as the proposed actions for the South End Railroad Project would be carried out within the existing railroad right-of-way, where freight service was previously in operation.

If a proposed action is not fully addressed in the South End Railroad PEA, the PEA will serve as a general document from which Supplemental Environmental Assessments (SEAs) and their corresponding Findings of No Significant Impact would tier to ensure compliance with NEPA.  If FEMA determines, during the preparation of an SEA, that a more detailed environmental review is warranted, FEMA will prepare a full EA.  If the EA indicates that the action would have significant impacts, FEMA will prepare an Environmental Impact Statement, as required by NEPA.  
Operation of independent freight service along the corridor may involve additional actions not described in the South End Railroad Project.  Such actions would be undertaken separately by NCRA, and are beyond the scope of this document. 

1.4	Purpose of and Need for Action
The purpose of and need for the action are described in Section 1.4 of the Flood PEA.  NCRA has determined that action is needed to protect public health and safety, restore damaged railroad facilities, minimize flood impacts, reduce future risks associated with damage to the railroad, and upgrade facilities to accommodate previous levels of service.  The purpose of the Proposed Action Alternative is to rehabilitate the railroad infrastructure so that the South End of the NWP may eventually be restored as an independently operated freight railroad.
1.5	Complementary Programmatic Documents
FEMA has programmatic documents and interagency coordination in place that support the material contained in the South End Railroad PEA. These documents are described in Section 1.5 of the Flood PEA.


2.0	ALTERNATIVE ANALYSIS
As part of this South End Railroad PEA, two alternatives have been put forth for discussion: the No Action Alternative and the Proposed Action Alternative.  These alternatives are described below. 
2.1	No Action Alternative

The No Action Alternative is discussed in Section 2.3.1 of the Flood PEA.  The No Action Alternative is defined as maintaining the status quo; FEMA would not provide funding for any actions.  Under this alternative, no funds would be available to implement proposed actions, and the repairs and modifications to the South Railroad would not be conducted. The existing railroad would continue to be inoperable, and certain facilities would remain vulnerable to future deterioration and damage.  Although this alternative is inherently inconsistent with FEMAs mission (if the action is otherwise eligible for FEMA program assistance), the No Action Alternative provides a benchmark against which the Proposed Action Alternative may be evaluated.

2.2 Proposed Action Alternative

The Proposed Action Alternative is described in Sections 2.3.5 and 2.5.6 of the Flood PEA.  For the South End Railroad project, the Proposed Action Alternative would involve repairing the railroad.

The Proposed Action may include the following types of individual actions:

* Replace and dispose of damaged ties using on-track mounted railroad equipment.

* Clean and reshape drainage ditches as necessary to restore to pre-disaster condition.

* Replace several at-grade crossing signal electronic components, replace gates that have been removed, upgrade the crossing surface if necessary, and reactivate the crossing protection equipment.

* Replace ballast that has been washed away or inundated with flood waters.

* Remove flood debris from drainage culverts or replace culverts that may have been damaged by flooding.

* Perform other structural upgrades such as upgrading the fixed bridge structural components within the railroad right-of-way.

* Transport material and equipment, as well as debris and other materials being disposed, using on-track mounted railroad equipment and railroad cars.

The actions listed below, which would also be completed under the project, as described in Appendix A, are categorically excluded from further review under NEPA pursuant to 44CFR 10.8 (d)(2) and are not addressed in the South End Railroad Project PEA.

* Use consultants to prepare contract documents and manage the procurement process;

* Use NCRA personnel to manage the consultants and provide oversight;

* Purchase railroad equipment; and

* Fit on-road equipment with hi-rail accessories.

2.3	Alternatives Eliminated from Further Consideration

Alternatives usually dismissed from further consideration in any of the environmental documents are those that require considerably more funding than available through FEMA programs or those that do not pass a cost-benefit analysis.  Other alternatives usually eliminated, after proper review and analysis, are those dismissed or rejected by the applicant for reasons such as cost limitations, impracticality of implementation, or incompatibility with local and state statutes.  If an SEA is prepared for individual action, it will address alternatives eliminated from further consideration, if any, and the justifications for rejection.


3.0	AFFECTED ENVIRONMENT AND ENVIRONMENTAL CONSEQUENCES
3.1	Geology, Geohazards, and Soils
3.1.1 	Affected Environment
The affected environment and regulatory framework for geology, geohazards, and soils is described in Section 3.1 of the Flood PEA.  The study area is located within the northern California Coast Ranges province (Section 3.1.1.2 of the Flood PEA).
3.1.1.1   Slope Instability

The northern California Coast Ranges region is primarily underlain by rocks of the Franciscan Complex.  This region is an area of active landform creation synonymous with widespread landsliding.  The Franciscan Complex comprises a suite of rocks that form the remains of an ancient ocean floor environment, including sandstone, chert, and mlange.  The last rock type is an often-chaotic mixture of blocks of sediments and ocean floor volcanic rocks.  Where the rocks are weak (in particular the deeply weathered mlange) large, deep landslides are common.  Landslides create a lumpy, uneven topography, and vegetation is dominated by grasslands.  Remnant unweathered blocks and more resistant rock types commonly form isolated rocky knobs or knockers in these areas of landsliding.

Mass wasting is downward movement of soils and rock under gravity.  This phenomenon includes landslides, rockfalls, and debris flows.  Mass wasting requires source materials, a slope, and a triggering mechanism.  Source materials include fractured and weathered bedrock and loose soils.  Triggering mechanisms include earthquake shaking, heavy rainfall, and erosion.  Slides and earth flows are landslides that can pose serious hazard to property in the hillside terrain of the Coast Ranges. They tend to move slowly and thus rarely threaten life directly.  When they movein response to such changes as increased water content, earthquake shaking, addition of load, or removal of downslope supportthey deform and tilt the ground surface.

Deep-seated landsliding, often occurring on slide planes located hundreds of feet below the surface and involving several square miles of hillside, is a result of the weak nature of the Franciscan bedrock and the over-steepening of slopes due to relatively rapid down-cutting of rivers as the Coast Ranges are uplifted.  Such landslides are perpetually moving, as river erosion is an ongoing process removing material from the base of these slopes, maintaining slope instability.  Examples of ongoing slope movement are common along the railroad corridor, especially between Cloverdale and Hopland.  Smaller-scale slope movements also occur on an almost annual basis as winter rains saturate shallow soils and colluvial deposits.  As these materials become water logged, they often lose mechanical strength and develop into shallow debris flows or soil slides.  These landslides are common where a cover of unconsolidated material occurs over relatively intact bedrock.  


3.1.1.2  Subsidence

Land surface subsidence can result from both natural and man-made phenomena.  Natural phenomena include subsidence resulting from tectonic deformation and seismically-induced settlements; soil subsidence due to consolidation; subsidence due to oxidation or dewatering of organic-rich soils and subsidence related to subsurface cavities.  Subsidence or settlement related to human activities include subsidence caused by decreased pore pressure due to the withdrawal of subsurface fluids, including water and hydrocarbons.

The potential for subsidence along the alignment of the South End Railroad Project has not been documented in detail.  Potential areas of concern may be along the northern shore of San Pablo Bay where historic subsidence, resulting from compaction of peat and water-saturated sediment, has been noted.  Evidence also indicates that this area is undergoing tectonic subsidence; however, this phenomenon is unlikely to have a major impact over time spans of engineering concern.

3.1.1.3	Seismic Hazards

The Coast Ranges is a region of moderate to high seismic activity.  With the exception of ongoing swarms of seismic activity in the geothermal area near Healdsburg known as The Geysers, present day seismicity is relatively low-level and associated with the known active faults.  The most significant earthquakes in this region historically have been the 1906 Great San Francisco earthquake on the San Andreas Fault and the 1969 Santa Rosa earthquakes on the Rodgers Creek Fault.  The latter event resulted in approximately $7 million damage in and around Santa Rosa.  Several brick and wood frame buildings in Santa Rosa were damaged beyond repair.

3.1.2	No Action Alternative

Under the No Action Alternative, erosion and the resulting loss of soil would continue to occur in areas where drainage ditches and culverts have been damaged or are blocked by debris.  Erosion and soil loss could cause slope failures and subsidence, resulting in deterioration of, or damage to, existing railroad facilities.  Failure to remove debris generated by prior railroad operation and maintenance could result in soil contamination as hazardous substances, such as lubricants, leach into the soil.  

3.1.3	Proposed Action Alternative

Impacts of Proposed Action Alternative are described in Sections 4.1.1.3 of the Flood PEA.  Construction activities may result in the disturbance of soils through excavation, heavy equipment use, debris clearing, vegetation removal, or similar actions.  Soil loss would occur directly from disturbance or indirectly via wind or water.  NCRA would implement Best Management Practices (BMPs), such as developing and implementing an erosion and sedimentation control plan, using silt fences or hay bales, revegetating disturbed soils, and maintaining site soil stockpiles, to prevent soils from eroding and dispersing off-site.  Conversely, cleaning and repairing culverts and drainage ditches would reduce the potential for uncontrolled erosion and soil loss. 

In some cases, slope failures could be triggered by some ground-disturbing actions occurring on steep slopes. To mitigate this potential, NCRA would review landslide potential before engaging in ground-disturbing actions.  NCRA would mitigate potential effects by appropriate siting of facilities and using proper geotechnical construction practices.

The Proposed Action Alternative would not have an impact on seismic hazards, nor would the activities undertaken alter the effects of seismic hazards to the facility.  The level of risk due to seismic activity would remain unchanged.  

3.2	Air Quality
3.2.1	Affected Environment
The affected environment and regulatory framework for air quality is described in Section 3.2 of the Flood PEA.  The South End Railroad Project falls within the San Francisco Bay Area, Northern Sonoma, and Mendocino air quality management districts.

3.2.2	No Action Alternative

Impacts of the No Action Alternative are described in Section 4.1.2 of the Flood PEA. The No Action Alternative would have no effect on air quality because no construction activities would be implemented, no ground disturbance would occur, and the railroad would remain non-operational.

3.2.3	Proposed Action Alternative

Impacts associated with the Proposed Action Alternative are discussed in Section 4.1.2 of the Flood PEA.  Short-term, local impacts to air quality from construction activities would likely include fossil fuel use for construction equipment, use of materials containing Volatile Organic Compounds (VOCs), and emissions of particulate matter smaller than 10 microns in diameter (PM10) from soil disturbance and debris removal.  Fossil-fuel use for construction equipment would produce emissions of carbon monoxide (CO), nitrogen oxides (NOx), PM10, particulate matter smaller than 2.5 microns in diameter (PM2.5), sulfur dioxide (SO2), VOCs, and hazardous air pollutants. VOCs and hazardous air pollutants emissions could also occur at construction sites from the use of paints, thinners, or solvents. 

The modification of previously permitted facilities or the construction of a new facility that includes new or modified stationary sources (for example, fossil fuel-fired electrical generators) would have the potential to increase the level of air pollutants beyond the threshold established by the local air quality district.  If this situation occurs, NCRA would apply for and obtain a pre-construction permit from the local air quality district and use best available control technologies, if required. 

NCRA would also be responsible for applying for and obtaining permits required under New Source Review and Prevention of Significant Deterioration review, if required. Railroad ties may not be burned without special air emission controls. 

Regardless of whether a permit is needed, NCRA would employ minimization measures to limit emissions, fugitive dust, and exhaust.  These measures may include: 

* Watering disturbed areas; 

* Spraying dirt roads with water during dry and windy days; 

* Maintaining and covering spoil piles;
 
* Scheduling staging area siting to minimize fugitive dust;
 
* Capping or carefully maintaining locomotive sanding towers to prevent sand loss; 

* Using crusting compounds to contain open hopper cars; and 

* Keeping construction equipment properly tuned.  

Some local air quality districts enforce general prohibitory rules under the Clean Air Act that require these types of good housekeeping measures to be implemented. 

Before approval of any federal action, the General Conformity Rule (GCR) requires that the responsible federal agency make a determination of conformity with the State Implementation Plan.  NCRA would review all actions on behalf of FEMA to determine whether they qualify for one of the exemptions listed in the GCR.  The activities to be completed under the Proposed Action Alternative would likely qualify for an exemption either because the action would be one of the specifically exempted activities under the GCR, or because expected emissions from the activity would fall below specific emission thresholds at which a conformity analysis is required.

The following activities under the Proposed Action Alternative are assumed to be exempt according to GCR Applicability (40 CFR Part 51.853), item (c) (2) (iv):  routine maintenance and repair activities, including repair and maintenance of administrative sites, roads, trails, and facilities.  Nevertheless, FEMA conducted an analysis of pollutant emissions, using U.S. Environmental Protection Agency (USEPA) emission factors and conservatively assuming activities would take place each weekday for four months.  The analysis assumed the equipment used in the repair and maintenance activities would include one switch-type locomotive and one tracked loader.  Based on the analysis, the resulting emissions were deemed to be far below the de minimis levels for which a conformity analysis would be required.

In the event that the proposed action goes substantially beyond what was assumed for the current analysis, or is found not to be exempt, NCRA would conduct an air quality analysis in conformance with GCR requirements to demonstrate that the proposed action would not:

* Adversely affect or delay air quality plan maintenance;

* Contribute to any new violations of an air quality standard;

* Increase the frequency or severity of an existing violation; or

* Delay achieving attainment or emission reductions in any area.

FEMA would document the results of this air quality analysis in an SEA for the action in question.

3.3	Hydrology and Water Quality 

3.3.1 Affected Environment

The affected environment and regulatory framework for hydrology and water quality are described in Section 3.3 of the Flood PEA.  The study area lies mostly within the Russian River watershed, with the exception of the southern quarter of the study area, which lies within watersheds that drain into San Pablo Bay; and the northernmost segment near Willits, which lies within the Eel River watershed.  The main stem of the Russian River, bordered to the west by the Coast Range, is approximately 110 miles long.  From its headwaters north of Ukiah, the river flows in a southeastward direction, turning to the west south of Healdsburg before emptying into the Pacific Ocean at Jenner.  Major tributaries to the Russian River include the East and West forks of the main stem, Robinson Creek, Feliz Creek, Pieta Creek, Big Sulphur Creek, Dry Creek, Maacama Creek, Mark West Creek, and Austin Creek. The Petaluma River, Sonoma Creek, Novato Creek, and San Antonio Creek flow south into San Pablo Bay.  Tributary streams in all watersheds are both perennial and ephemeral.  The segment of the railroad between Ignacio and Schellville in Marin and Sonoma counties is located in the vicinity of wetlands that border San Pablo Bay.
3.3.2	No Action Alternative
Impacts of the No Action Alternative are described in Section 4.1.3.1 of the Flood PEA. Under the No Action Alternative, hydrology and water quality have the potential to be negatively affected by future floodwaters coming into contact with existing pollutant sources if no action is taken to restore the railroad and its drainage system (drainage ditches and culverts) to pre-disaster condition.  Existing conditions along the railroad include areas of potential erosion that may cause sedimentation of waterways.  Drainage ditches and culverts containing flood debris will slow and/or block future floodwaters if they are not cleaned or replaced, causing a back up of water out of the floodplain that may come into contact with pollutants.


3.3.3	Proposed Action Alternative
Impacts of the Proposed Action Alternative are described in Section 4.1.3.3 of the Flood PEA. Most of the activities to be conducted under the Proposed Action Alternative would not occur within rivers, streams, or wetlands.  However, construction activities may result in the disturbance of soils, which if transported into water bodies could affect water quality.  BMPs would be employed to reduce erosion and prevent or reduce the amount of sediment entering water bodies.
The following activities may result in work in or near water bodies:
* Removing flood debris from culverts and replacing culverts damaged by flooding;
* Upgrading structural components of bridges; and
* Rebuilding the fender system on the Black Point Bridge over the Petaluma River. 
The minimization measures described in Section 3.5.3.1 below would reduce or eliminate the impacts of these activities to water quality.  The cleaning, repair, and replacement of culverts and the cleaning of drainage ditches would improve water quality by reducing erosion and soil loss and eliminating debris that provides potential sources of contaminants.
Prior to implementing specific actions affecting water bodies, NCRA must obtain the following permits, as appropriate: 
* Section 404 permit from the U.S. Army Corps of Engineers, for construction activities within Waters of the United States; 
* Section 401 water quality certification or waiver from the North Coast Regional Water Quality Control Board; and
* Streambed Alteration Agreement from the California Department of Fish and Game, for work affecting the stream banks and channels.

3.4	Floodplain Management 

3.4.1 Affected Environment

The affected environment is described in Section 3.4 of the Flood PEA.  In compliance with Executive Order (EO) 11988, Floodplain Management, and FEMAs implementing regulations (44 CFR Part 9), FEMA must avoid short- and long-term impacts associated with the occupancy and modification of floodplains to the extent practicable. According to Flood Insurance Rate Maps published by FEMA, parts of the railroad alignment between Willits and Lombard are located within the 100-year floodplain, or border the floodplain. 

3.4.2 No Action Alternative

Impacts of the No Action Alternative are described in Section 4.1.4.1 of the Flood PEA.  
Under the No Action Alternative, there would be no direct impact to the floodplain. Drainage ditches would not be cleared, and culverts would not be repaired or cleaned. By not maintaining or improving drainage, the railroad would continue to be subject to damage during storms that cause heavy runoff and stream flooding.

3.4.3 Proposed Action Alternative

Impacts of the Proposed Action Alternative are described in Section 4.1.4.3 of the Flood PEA.  Because portions of the railroad are located in the 100-year floodplain, the railroad would continue to be susceptible to damage caused by floods.  However, it is not practicable to move the railroad alignment from the floodplain.  Additionally, the proposed modifications are minor in nature and do not increase the impact of the facility on the floodplain.

Under the Proposed Action Alternative, drainage along the railroad would be improved by clearing drainage ditches and repairing and cleaning culverts, reducing the potential for future damage during storms.  However, none of the activities in the Proposed Action is expected to change the function of the floodplain or change base flood elevations.  The proposed culvert modifications are not expected to affect downstream discharges during a 100-year flood event.  Because the crossings would be overtopped by larger flood events, clearing, repairing, or replacing culverts at these crossings would have no substantial effect on downstream discharges, provided that culvert sizes are not substantially increased.  This condition would be consistent with that of the current crossings, which in most cases are similarly overtopped by smaller, more frequent flood events.  

In compliance with EO 11988 and 44 CFR Part 9, FEMA would publicly circulate a notice describing the Proposed Action and reasons for undertaking certain activities in the floodplain.
3.5 Biological Resources
3.5.1 Affected Environment

The affected environment is described in Sections 3.5 and 3.6 of the Flood PEA.  

A U.S. Fish and Wildlife Service (USFWS) list of federally listed endangered, threatened, proposed, and candidate species was compiled for the 27 U.S. Geological Survey (USGS) 7.5-minute quadrangles covered by the study area (see Appendix B).  In addition, a California Natural Diversity Data Base (CNDDB) search was conducted for a five-mile radius of the study area.  Using these resources, a comprehensive table listing the special status species with potential to occur in the vicinity of the study area has been prepared.  The table is presented in Appendix B.  


3.5.1.1	General Habitat Types

Annual Grasslands.  Grasslands are herbaceous communities dominated by annual or perennial grasses and forbs (broad-leaved plants).  Annual grasslands are dominated by a sparse to dense cover of annual grasses interspersed with native annual and perennial forbs. Dominant species include soft chess (Bromus hordeaceus), wild oats (Avena spp.), slender fescue (Vulpia bromoides), hare barley (Hordeum murinum ssp. leporinum), silver hair grass (Aira caryophyllea), dogtail (Cynosurus echinatus), and ripgut brome (Bromus diandrus). Annual forbs interspersed among the grasses include blue-eyed grass (Sisyrinchium bellum), clover (Trifolium sp.), common fiddleneck (Amsinckia intermedia), Pursh's lotus (Lotus purshianus var. purshianus), tarplant (Hemizonia congesta ssp. clevelandii), baby blue-eyes (Nemophila menziesii var. menziesii), and johnny tuck (Triphysaria eriantha var. eriantha). Perennial species include narrow-leaved onion (Allium amplectens), elegant harvest brodiaea (Brodiaea elegans ssp. elegans), self heal (Prunella vulgaris ssp. lanceolata), yarrow (Achillea millefolium), common soap plant (Chlorogalum pomeridianum var. pomeridianum), and California oat grass (Danthonia californica).

Oak Woodlands.  Woodland communities are dominated by deciduous hardwood trees and usually support herb and shrub layers.  Oak woodlands are regionally common and are found in Marin, Sonoma and Mendocino counties.

Oak woodlands generally contain various mixtures of Oregon Oak (Quercus garryana), black Oak (Q. kelloggii), Garry oak (Q. garryana), California buckeye (Aesculus californica), California bay (Umbellularia californica), Bigleaf Maple (Acer macrophyllum), madrone (Arbutus menziesii), and Douglas-fir (Pseudotsuga menziesii var. menziesii ).  To a lesser extent, valley oak (Q. lobata) is found in the study area.  The shrub layer varies from dense to sparse and consists of common manzanita (Arctostaphylos manzanita), poison oak (Toxicodendron diversilobum), deer brush (Ceanothus integerrimus), and ocean spray (Holodiscus discolor).  Herbaceous cover is typically 40 percent to 80 percent, depending on shrub and canopy density, and is usually dominated by perennial grasses.

Woodland structure and species compositions appear to vary with different site conditions.  For example, on rocky south-facing slopes with shallow soils, oak woodlands have sparse tree, shrub, and herb layers.  On moist, undisturbed sites, oak woodland has a nearly closed tree canopy with a dense understory of shrubs, perennial grasses, and forbs.

Mature oak woodland in the study area are especially attractive to wildlife because they provide important forage and cover for a large number of ground-, shrub-, and tree-nesting species, including raptors such as golden eagles (Aquila chrysaetos), Cooper's hawks (Accipiter cooperii), sharp-shinned hawks (Accipiter striatus), and white-tailed kites (Elanus leucurus).

Woodpeckers excavate nestholes in live and dead oaks.  These cavities are subsequently used by other cavity-nesting species, such as American kestrels (Falco sparverius), western screech-owls (Otus kennicottii), tree swallows (Tachycineta bicolor), ash-throated flycatchers (Myiarchus cinerascens), white-breasted nuthatches (Sitta carolinensis), plain titmice (Parus inornatus), and western bluebirds (Sialia mexicana).

Riparian Communities.  Riparian communities are found along creeks, rivers, drainages, fence rows, and at other scattered locations throughout the study area, on tributaries of the Eel, Russian, Petaluma, and Napa Rivers.  Riparian communities are characterized by plant communities ranging from multi-layered woodlands to dense scrub thickets.  Within the same plant community type, some riparian communities occur in moister soils and support more hydrophytic species in the shrub and herbaceous layer than other areas in the same plant community.  The dominant species in the canopy layer are cottonwood (Populus sp.), California sycamore (Platanus racemosa), and valley oak.  Subcanopy trees are white alder, boxelder (Acer negundo ssp. californicum), and Oregon ash.  Typical understory shrub layer plants include poison-oak, buttonbrush, and willows (Salix sp.).  The herbaceous layer consists of sedges, rushes, grasses, miners lettuce, poison-hemlock, and hoary nettle.

Riparian habitats support the most dense and diverse bird communities in northern California and in the study area. The variety of plant species, multi-layered vegetation, perennial surface waters, and variety of foods makes riparian habitats especially attractive to wildlife (Warner 1979).  Mature tree willows (Salix sp.), valley oaks, black oaks, and Oregon ash (Fraxinus latifolia) provide high-quality nesting habitat for raptors, such as red-tailed hawks (Buteo jamaicensis), red-shouldered hawks (Buteo lineatus), and white-tailed kites, and for cavity-nesting birds that require mature stands of trees, such as the Nuttall's woodpeckers (Picoides nuttallii), downy woodpeckers (Picoides pubescens), northern flickers (Colaptes auratus), plain titmice (Parus inornatus, and white-breasted nuthatches (Sitta carolinensis). 

Scrub/shrub willows are dominated by low-stature plants and lack the multi-layered vegetation of most other riparian types. Although scrub/shrub willow communities tend to support fewer wildlife species than mixed riparian woodland communities, they do offer important cover for deer and a variety of breeding and migratory songbirds, such as flycatchers, vireos, and warblers. 

California grapevines (Vitus californica), blackberries (Rubus sp.), blue elderberries (Sambucus mexicana), valley oak, and black oaks produce important fall and winter foods for birds and mammals. Common wildlife species that depend on the nectar, fruits, and seeds of these riparian plants include Anna's hummingbirds (Calypte anna), black-headed grosbeaks (Pheucticus melanocephalus), rufous-sided towhees (Pipilo erythrophthalmus), California towhees (Pipilo crissalis), raccoons (Procyon lotor), striped skunks (Mephitis mephitis), gray foxes (Urocyon cinereoargenteus), and western gray squirrels (Sciurus griseus).

Because many riparian communities are relatively scarce compared to their historic extent and because they provide important foraging and nesting habitat for many resident and migratory wildlife species, these communities qualify as sensitive natural communities.

Mixed North-Slope Forest.  This habitat type is mostly found in the Little Lake Valley near Willits.  Forest communities are dominated by tree species with canopy cover that generally exceeds 60 percent and is often nearly 100 percent.  Forests are distinguished from woodlands by their more densely vegetated canopies, well-developed shrub layer, and scant herbaceous layer.  The mid- and upper-canopy layers provide foraging, nesting, and roosting substrates for a diversity of wildlife, including several special status species such as northern spotted owls.

Mixed north-slope forests are characterized by a multi-layered overstory dominated by black oak, madrone, and California bay, intermixed with occasional Douglas-fir and canyon live oak (Quercus chrysolepis). The shrub layer is dominated by deer brush, poison oak, common manzanita, mountain mahogany (Cercocarpus betuloides), creeping snowberry (Symphoricarpos mollis), and ocean spray. The shrub layer is dominated by species that also inhabit the nearby mixed chaparral community. Some mixed north-slope forests contain dense understory stands of manzanita (Arctostaphylos sp.) and poison oak. This community is similar in species composition to mixed evergreen forests, except the former has a canopy with greater than 40 percent deciduous oak cover and the latter has a canopy with a greater percentage of madrone, tan oak (Lithocarpus densiflorus), California bay, and Douglas-fir.

Wet Meadow.  Wet meadows are found in both natural and artificial settings in the study area. They develop in areas where the soil and vegetation have remained undisturbed (or only minimally disturbed) for many years.  Under natural conditions, wet meadows in the foothill and valley portions of the study area are found in swales, drainages, areas of springs and seeps, and along terraces and alluvial fans. In artificial settings, this herbaceous community is found in drainage ditches and in depression created by excavation.

Sedges and rushes comprise approximately 40 to 80 percent of the total hydrophytic vegetation in wet meadows.  Other dominant species include redtop (Agrostis stolonifera), meadow-foxtail (Alopecurus pratensis), California oatgrass, creeping ryegrass, Kentucky fescue, pennyroyal (Mentha pulegium), Timothy grass (Phleum pratense), western buttercup (Ranunculus occidentalis), curly dock (Rumex crispus), common velvet grass (Holcus lanatus), and birds-foot trefoil (Lotus corniculatus).  In addition, ash and valley oak trees are found sporadically in some wet meadows. 

These wetlands receive water from various sources, including agricultural field and pasture irrigation, creek floodplain aquifers, overbank flooding and sheet drainage from excessive runoff, groundwater springs, and shallow groundwater during winter, spring, and early summer.

The high plant diversity and variable hydrologic characteristics of wet meadows make them attractive foraging, nesting, and resting habitat for many wetland-dependent birds, reptiles, and amphibians. The mosaic of dry meadows, marshes, and open water near most of these wet meadows enhances their value for wildlife; however, because wet meadows are associated with saturated soils, they receive limited use by most species of small mammals and their predators.

Vernal Pools.  Vernal pool plant communities are restricted to particular landforms and soil profiles in the valley portions of the study area. The habitat develops primarily within depressions on high terraces with heavy clay subsoil horizons.  Vernal pools are small, internally drained basins that collect rainfall and surface runoff from a surrounding grassland watershed.  An impervious layer of subsoil prevents water from infiltrating the soil profile, causing it to form shallow, perched water tables that are exposed in small depressions. The frequency and duration of ponding and saturation vary among vernal pools due to the size of the basin and its watershed, depth to the impervious subsoil layer, and the timing and amounts of rainfall during each wet season.

Characteristic annual hydrophytes include bracteate popcornflower (Plagiobothrys bracteatus), purslane speedwell (Veronica peregrina ssp. xalapensis), speedwell (Veronica anagallisaquatica), downingia (Downingia sp.), Bolanders water-starwort (Callitriche heterophylla var. bolanderi), common toad rush (Juncus bufonius var. bufonius), Bakers meadowfoam, Douglas meadowfoam (Limanthes douglasii ssp. nivea), semaphore grass (Pleuropogon californicus), and field owls clover (Castilleja campestris).  Herbaceous perennials include spreading rush (Juncus patens), slender-beaked sedge (Carex athrostachya), green-sheath sedge (Carex feta), meadow-foxtail (Alopecurus pratensis), Timothy grass (Phleum pratense), pennyroyal (Mentha pulegium), and curly dock (Rumex crispus).

Vernal pools provide foraging habitat, breeding habitat, and cover for a small number of vernal-pool-dependent wildlife species. Although vernal pools are ephemeral aquatic habitats, many invertebrates and amphibians have adapted to, and are dependent on, this resource. 

Vernal pools are identified as sensitive natural communities because they provide habitat for a variety of special status plant and wildlife species and have been heavily degraded and greatly diminished in area as a result of agricultural and urban development, water projects, and grazing. Many of the remaining vernal pools in California are threatened by conversion to agricultural and urban uses. The CNDDB designates this type of wetland as a community of highest inventory priority because of its value to wildlife and because of ongoing threats to its existence in many areas (CNDDB 2003).

Stream Channels.  Stream channels in the study area are typically rocky and unvegetated.  This community type includes intermittent and perennial stream channels.  These stream channels may provide habitat for migrating adult and juvenile salmonids, although some spawning and seasonal rearing may occur.  These areas lack hydrophytic vegetation but are considered jurisdictional waters of the United States.

Tidal Salt Marshes.  The San Francisco Bay, including San Pablo Bay, contains the largest salt marsh systems in the state (CNR 2003).  Salt marsh plants are adapted to a harsh, semi-aquatic environment and saline soils.  Species diversity is low.  Stout stems, small leaves, and physiological adaptations for salt excretion and gas exchange characterize the inhabitants of the salt marsh, which are mostly grasses and low perennial herbs. The tangle of marsh plant roots and stems helps to stabilize the muddy bottom, as well as to trap debris and dissolved nutrients with each tidal cycle.  Bacteria convert this oasis of detritus into food resources for microscopic algae, invertebrate larvae, and larger animals. 

Species composition and zonation in the salt marsh are governed by salinity gradients in combination with the amount of intertidal exposure.  Eelgrass (Zostera marina) occupies the lowest or most marine zone because it cannot tolerate a freshwater environment or intertidal conditions that would expose its roots to air.  Cordgrass (Spartina foliosa) occurs in the marine-to-terrestrial transition zone, characterized by lower salinity and periodic exposure to the air.  Inland, where conditions are even drier, pickleweed species (Salicornia sp.) are common.  On higher ground, where tidal intrusions are rare, jaumea (Jaumea carnosa), shoregrass (Monanthochloe littoralis), sea arrowgrass (Triglochin maritima), and the endangered salt marsh bird's beak (Cordylanthus maritimus) are found (CNR 2003).  Saltgrass (Distichlis spicata) is widespread, occurring from the middle to high marsh, as well as in dunes and on salt flats.  The orange, parasitic dodder (Cuscuta salina) frequently invades and covers large areas of vegetation (CNR 2003). 

Developed Areas.  Developed areas include road and railroad corridors and areas of dominated by residential, commercial, and industrial development.

3.5.1.2	Regional Areas

The habitat types described above are found in the geographic regions described in this section.

Little Lake Valley.  Little Lake Valley is dominated by annual grasslands, oak woodlands, mixed north-slope forest, riparian communities, wet meadows, streams and channels.  The City of Willits is located in Little Lake Valley.

Ukiah Valley.  The Ukiah Valley historically supported a rich diversity of oak woodlands and forests.  Valley oaks commonly exist in this valley.  At the present time, no valley oak woodland remains in the Ukiah Valley (Mendocino County 2003).  A few patches of valley oak riparian woodland are found on some creeks in the area, but this plant community no longer exists along the Russian River in the Ukiah Valley (Mendocino County 2003).  Interior live oak woodlands remain in the eastern hills of the valley.  Healthy stands of black oak woodlands are found in the western portions of the City of Ukiah and the western hills.  Even the chaparral community, a complex of trees and shrubs, includes shrub interior live oak, scrub oak, and leather oak (Mendocino County 2003).

Russian River Valley from Hopland to Healdsburg.  The area surrounding the Russian River from Hopland through Healdsburg is dominated by annual grasslands, oak woodlands, and riparian corridors.  Agricultural areas dominated by vineyards are also found within the Russian River floodplain and the adjacent low elevation hillsides.  Grape production in the area has increased dramatically in the past decade, and has resulted in the conversion of land not previously used for agriculture. The transition from agricultural areas to other habitat types is typically abrupt, but occasionally individual oak trees are left intact within or near the edges of vineyards.  Seeps, seasonal wetlands, irrigation ponds may also be found in this area.

In Mendocino County, grasslands are often maintained by cattle grazing in areas that might otherwise develop forest or chaparral communities.  Grasslands commonly grade into various shrub and tree habitats.  

Blue oak woodland is an increasingly rare habitat found in Californias foothills (Mendocino County 2003).  However, it is common east of State Route 101 from Ukiah to the Sonoma County line, including the area east of Hopland.  Blue oak communities normally occur on dry, rocky slopes in infertile soils where others oak species do not flourish.  Conditions are typically too harsh to support other hardwood or oak species.

Santa Rosa Plain.   The Santa Rosa Plain is characterized by open grassland with scattered stands of oak.   This plain is an area of dense, impervious clay soil, naturally interconnected shallow ponds and vernal pools, and scattered oaks.  This area contains unique vernal pool habitats that support one of the highest rates of endemic species of any habitat type in Sonoma County (CNPS letter 2003).

Petaluma Valley.  The Petaluma Valley contains grassland, oak woodland, riparian communities, small vernal pools, and marsh habitats.  It contains the largest remaining intact tidal marsh within the San Francisco Bay estuary (Wetland Campaign 2003).  Many of the natural features in it are characteristic of the estuary's historic marshes.  The Petaluma Marsh presents nursery habitat for young salmon, trout, and other fish and aquatic species native to the bay.  The Petaluma River flows into northwestern San Pablo Bay.  Large vernal pools are also known to exist in the vicinity of Petaluma (CDFG 2003).

San Pablo Bay Shoreline.  The area from Ignacio to Schellville includes open grasslands and pasture, limited oak woodlands, extensive paved areas, residential, and commercial development.  It also contains salt marshes and sloughs near San Pablo Bay, and riparian communities along streams and creeks.  However, the pristine landscape and its associated vegetation cover (such as oak woodland, savanna, and open grassland) have been almost completely displaced in the study area, first by agriculture and more recently by residential and commercial development.  Weedy, non-native annual grasslands are abundant.  Extensive salt marshes exist along the lower Petaluma River.

Napa River Area. Within the study area, the Napa River area includes a series of streams, sloughs, and tidal salt marshes.  The lower Napa River area is surrounded by the Napa-Sonoma Marshes Widlife Area on the west side.  Skaggs Island is located southwest of the railroad alignment.  The area north of the alignment includes non-native grasslands, limited oak woodlands and riparian areas, and paved areas.

3.5.1.3	Special Status Species

The table in Appendix B provides information regarding special status species with potential to occur in the study area.

Fish.  Special status fish species include:  

* Green sturgeon (Acipenser medirostris)
* Tidewater goby (Eucyclogobius newberryi)
* Southern Oregon/Northern California coho salmon (Oncorhynchus kisutch)
* Central California coast coho salmon (Oncorhynchus kisutch)
* Central California coast steelhead (Oncorhynchus mykiss)
* Northern California steelhead (Oncorhynchus mykiss) 
* California coastal chinook salmon (Oncorhynchus tshawytscha) 
* Sacramento splittail (Pogonichthlys macrolepidotus)

The National Marine Fisheries Service (NMFS) is currently reviewing its critical habitat designations for anadromous fish.  Currently, there are no critical habitat designations for any of these special status fish in California (NMFS 2003).

Along the railroad alignment, special status fish species are likely to occur in the areas described in Table 1.

Table 1
Segments in Areas with Potential to Support Special Status Fish Species

NRCA Segment
Watershed
Special Status Fish
From Willits to approximately 5 miles south 
Eel River and its tributaries (Baechtel, Sherwood, and Outlet Creeks)
* Northern California steelhead
* Southern Oregon/Northern California coast coho salmon
* California coastal chinook salmon
Approximately 5 miles south of Willits through Cotati
Russian River
* California coastal chinook salmon 
* Central California coast coho salmon 
* Central California coast steelhead
From Penngrove to Ignacio
Petaluma River, San Antonio Creek, and Novato Creek
* Central California coast steelhead 
* Green sturgeon (Petaluma River only)
San Pablo Bay shoreline from Ignacio to Sonoma Creek
Sloughs, coastal lagoons, and lower stream reaches
* Sacramento splittail 
* Tidewater goby
Sonoma Valley to Schellville
Sonoma Creek
* Central California coast steelhead
Schellville to Lombard
Napa River
* Central California coast steelhead
* Green sturgeon
* Tidewater goby
* Sacramento splittail


Amphibians.  Two special status amphibians have the potential to occur in the study area: the California red-legged frog (Rana aurora draytonii); and the California tiger salamander (Ambystoma californiense).  Both species require freshwater resources, such as streams, rivers, vernal pools, stock ponds, or seasonal ponds, in which to breed.  The tiger salamander may disperse through annual grasslands.  Red legged-frogs disperse upstream and downstream in search for suitable estivation sites, such as riparian areas (CDFG 2003).  These two amphibians may occur within portions of the study area.  Figure 2 shows the areas in which the California tiger salamander is listed as a proposed threatened species.  The California red-legged frog is listed as endangered in the Central Valley hydrographic basin (including the Sacramento, San Joaquin, Kings, Kaweah, and Kern River systems) and from the Santa Clara River system south to the Mexican border; it is listed as threatened in the remainder of its range in California (CDFG 2003).  The red-legged frogs historical range extends through the Pacific slope drainages from the vicinity of Redding (Shasta County) inland and at least to Point Reyes (Marin County) southward to the Santo Domingo River drainage in Baja California, Mexico (CDFG 2003).  Red-legged frogs are still locally abundant within portions of the San Francisco Bay area.  

As shown in Figure2, a known California tiger salamander breeding population exists in Santa Rosa east of Highway 101 but west of Highway 116, near Highway 12 (USFWS 2002).  The breeding population occurs mostly near Highway 12, but salamander are known to disperse through surrounding areas as well.  Migrations to and from breeding ponds may exceed 1,000 m (3,300 ft) (CDFG 2003).  

Birds.  Special status bird species include:

* Marbled murrelet (Brachyramphus marmoratus)
* Western snowy plover (Charadrius alexandrinus nivosus)
* Western yellow-billed cuckoo (Coccyzus americanus)
* Bald eagle (Haliaeetus  leucocephalus)
* California clapper rail (Rallus longirostris obsoletus) 
* Northern spotted owl (Strix occidentalis caurina)

Critical habitat for the marbled murrelet and the northern spotted owl has been designated in the vicinity of Willits.

Locations of habitat that may support these species are given in Table 2.

Table 2
Locations with Potential to Support Special Status Birds

Likely Locations Within Study Area
Habitat
Special Status Bird
Little Lake Valley 
Mature, coastal coniferous forest for nesting
Marbled murrelet
Little Lake Valley 
Nests in upper canopy of large trees, usually conifers. Also nests on bridges and buildings in urban areas.  Winters near lakes, reservoirs, river systems, and coastal wetlands on protected cliffs.
Bald eagle
Little Lake Valley 
Old-growth forests or mixed stands of old-growth and mature trees
Northern spotted owl
Ukiah, Russian River, Petaluma, and Napa valleys
Deciduous riparian thickets or forests
Western yellow-billed cuckoo
San Pablo Bay shoreline
Sandy beaches, salt pans, coastal dredged spoil sites, dry salt ponds, salt pond levees, and gravel bars
Western snowy plover
San Pablo Bay shoreline
Tidal salt marshes near tidal sloughs
California clapper rail

Mammals.  The table in Appendix B lists one mammal species  the salt marsh harvest mouse (Reithrodontomys raviventris), with the potential to occur in the study area.  This species' preferred habitat is pickleweed saline emergent wetlands.  This species is known to occur in the San Francisco Bay and its tributaries, on the Marin Peninsula, through Petaluma, Napa, and Suisun Bay marshes.

Invertebrates.  Four special status invertebrates have the potential to occur in the study area.  These species include: vernal pool fairy shrimp (Branchinecta lynchi), Callippe silverspot butterfly (Speyeria callippe callippe), Myrtles silverspot butterfly (Speyeria zerene myrtleae), and the California freshwater shrimp (Syncaris pacifica).

Plants.  As listed in Appendix B, eighteen plant species have the potential to occur in the study area.  Four special status plants occur nowhere else except in the Santa Rosa plain:  Bakers stickyseed (Blennosperma bakeri), Sebastopol meadowfoam (Limnanthes vinculans), Burkes goldfields (Lasthenia burkei), and many-flowered navarretia (Navarretia leucocephala ssp. plieantha) (CDFG 2003).  Critical habitat for the Bakers larkspur has been proposed (but not designated) in the vicinity of Petaluma.

3.5.2 No Action Alternative

Relevant impacts associated with the No Action Alternative are discussed in Sections 4.1.5.1, 4.2.5.1, and 4.4.5.1 of the Flood PEA.  No federal undertaking would occur under this alternative; therefore there would be no requirement for compliance with Section 7 of the Endangered Species Act.  Federally listed threatened or endangered species would not be adversely affected, nor would suitable habitat for such species be adversely affected, except where degradation of the environment (including critical habitat) continues to occur.  

3.5.3 Proposed Action Alternative

Relevant impacts associated with the Proposed Action Alternative are discussed in Sections 4.1.5.3 and 4.1.6.3 of the Flood PEA. 

If NCRA proposes to undertake activities that could affect federally listed species as described below, FEMA must be notified before these activities commence.  As the lead federal agency, FEMA would consult with either USFWS or NMFS as appropriate; prepare Biological Assessments if required;  and require that NCRA implement any mitigation measures defined by USFWS or NMFS during consultation.
 
3.5.3.1	Potential Impacts to Fish

Along its entire length between Lombard and Willits, the existing railroad alignment crosses numerous water courses, both perennial and ephemeral, most of which have historically supported anadromous fish.  Additionally, between Schellville and Petaluma, the alignment crosses or lies adjacent to sloughs and other water bodies associated with the estuaries and salt marshes of San Pablo Bay.  Activities with the potential to directly affect fish species include repair, replacement, or cleaning of culverts and   
modifications to existing bridges, including the reconstruction of the fender system at Black Point Bridge on the Petaluma River.  Other activities along the railroad alignment, such as replacing ballast, may affect fish species indirectly through discharge of sediment or other material into water bodies.  In-stream activities may affect fish migration or result in take of individuals.  Potential impacts of excessive sediment include smothering eggs and trapping fry (newly hatched fish) in gravel beds.  Activities involving culverts and bridges have the potential to affect federally listed species in the areas described in Table 1. 

Temporary diversion of flowing streams that may contain anadromous fish species would require consultation with NMFS and the preparation of an SEA. 

To reduce potential impacts to fish species, NCRA would implement the following minimization and avoidance measures:

* No heavy machinery would be operated within the channel of a watercourse.

* Ground disturbing activities within stream channels and along stream banks would occur outside of the rainy season (that is, between June 1 and October 1). 

* Construction debris would not be discharged into any aquatic resource.  Any material that falls into a stream during construction would be removed in a manner that has a minimum effect on the streambed and water quality.

* Erosion control measures would be implemented during construction to reduce or eliminate possible discharge of sediment into aquatic resources.  These measures include, but are not limited to, installing silt fences or other detention methods immediately downgradient of disturbed areas.

* Spill prevention measures would be implemented during construction.

* Repair of culverts and stream crossings on permanent streams shall be designed to pass adult and juvenile salmonid species (coho, chinook, and steelhead).  NCRA shall adhere to either the California Department of Fish and Games Culvert Criteria for Fish Passage (2003) or The National Marine Fisheries Service Guidelines for Salmonid Passage at Stream Crossings (2001).


3.5.3.2 Potential Impacts to Amphibians

Activities undertaken in or adjacent to streams or other aquatic resources that may provide habitat for California red-legged frog and California tiger salamander could result in adverse impacts.  The minimization and avoidance measures described in Section 3.5.3.1 above would reduce potential impacts to these species.  In addition, construction activities during the breeding season (November through March) would be avoided.

As stated in Section 3.5.2 above, tiger salamanders are known to disperse up to 1,000 meters from breeding ponds.  Given that the railroad alignment is located approximately 1.5 miles east of the known population in the vicinity of Santa Rosa, construction activities near the railroad alignment would be located a sufficient distance from the breeding and dispersal areas of this population to avoid adverse impacts.

3.5.3.3	Potential Impact to Birds

Birds may be affected through noise disturbance associated with construction activities for the South End Railroad Project.  USFWS considers the potential effects of noise disturbance on birds up to 0.25 mile from the noise source (Watkins 1999).  Noise disturbance can disrupt nesting activities, which could result in a take if fledgings are abandoned as a result.  Noise disturbance can also reduce breeding success and disrupt foraging activities.  Although noise generated from railroad repair work would be transient and non-permanent, it could adversely affect special status birds if it causes a specific adverse long-term or irreversible effect on the species.

Potential locations of suitable habitat for special status bird species are given in Table 2.  If suitable habitat for these species is found within 0.25 mile of construction activities, these activities should be initiated prior to the beginning of the breeding season (that is, prior to January 1) to minimize the effect of noise disturbance on nesting.  With implementation of this measure, noise disturbance would begin before birds choose nesting locations.  Birds would select nest sites away from the railroad in low-noise level areas.

Some avian species have been known to habituate to increased noise levels.  However, the timing of the introduction of the noise may be the key to whether species will continue to use the habitat.  If the noise disturbance is introduced outside the nesting season, birds may eventually become habituated to the disturbance and cease to flee a the onset of disturbance.  Once birds are habituated, nesting could occur without disruption from noise disturbance.  However, some species are very sensitive to disturbance, and it is unlikely that they would habituate. 

3.5.3.4	Potential Impact to Mammals

The proposed project has the potential to adversely affect the salt marsh harvest mouse, if salt marshes are found within the study area.  This habitat type may occur along the San Pablo Bay shoreline and should be avoided during construction activities.  If work is performed in salt marshes, a qualified biologist should identify the areas dominated by pickleweed (Salicornia sp.)  Silt fences should be placed around the pickleweed areas prior to starting construction.

3.5.3.5	Potential Impact to Invertebrates

If construction activities and staging areas are limited to the existing railroad alignment, no adverse effects to vernal pool fairy shrimp, Callippe silverspot butterfly or Myrtles silverspot butterfly are anticipated.  However, activities occurring outside the existing railroad alignment have the potential to affect these species.  

Vernal pool habitats may occur in the entire study area, but are more likely to occur in the Santa Rosa Plain.  The butterfly species may be adversely affected by the proposed project if their host plant (Viola sp.) is removed or destroyed.  This plant occurs in areas immediately adjacent to the coast, such as dunes, scrub, and grasslands along the San Pablo Bay shoreline.  If NCRA determines that work outside the existing alignment is necessary in these areas, surveys would be conducted to determine if these features exist.  If found, they would be fenced off and avoided.

Impacts to the California freshwater shrimp would be avoided if no work is conducted in vernal pools or perennial freshwater streams.  Implementation of the avoidance and minimization measures described in Section 3.5.3.1 above would reduce impacts to shrimp in perennial freshwater streams.
 
3.5.3.6	Potential Impact to Plants

Similarly, if construction activities and staging are limited to the railroad alignment and no vegetation is removed or destroyed, the proposed project will not adversely affect special status plants.  However, activities undertaken outside the railroad alignment and resulting in the removal of vegetation, such as use of staging areas, access areas, or areas planned for disposal of material, could affect special status plant species.  If these activities are undertaken in areas that provide suitable habitat for these species, NCRA would conduct plant surveys during the blooming period of the identified special status plants.  This task would be performed by a qualified biologist.  If any of these special status plants is identified during the surveys, populations of these species would be fenced off and avoided.

3.6 Cultural Resources

3.6.1	Affected Environment
The affected environment is described in Section 3.7 of the Flood PEA.  Because the proposed actions would be carried out within the existing railroad right-of-way, FEMA has determined that the area of potential effect (APE) for the project is defined as the NCRA right-of-way from Willits (MP 142.5) south to Lombard (MP 1). 
A Programmatic Agreement (PA) is in place between FEMA, OES, and the State Historic Preservation Officer (SHPO) for FEMA-1203-DR-CA.  Appendix 1 of the PA specifies certain activities that are programmatically excluded from further review by the SHPO.  These actions include replacement-in-kind projects and those projects where activities are confined to areas previously disturbed. 
The NWP, including all of its associated components, is itself a cultural resource that passes through regions of California that vary in sensitivity for both prehistoric and historic cultural resources.  When a specific action is identified that would be using FEMA funds, it would be considered an undertaking for purposes of compliance with Section 106 of the National Historic Preservation Act (NHPA).

3.6.2 	No Action Alternative

Impacts of the No Action Alternative are described in Section 4.1.7.1 of the Flood PEA.  Under this alternative, no action would be undertaken to repair damage to the railroad.  Therefore, there would be no requirement for compliance with Section 106 of the NHPA.

3.6.3	Proposed Action Alternative

Impacts of the Proposed Action Alternative are described in Section 4.1.7.3 of the Flood PEA. Construction activities that are ground disturbing in nature would have the potential to significantly impact cultural resources located along the project corridor if they involve excavation in previously undisturbed soil or if items being repaired or replaced have attained a historic significance of their own. 

For the purpose of the South End Railroad PEA, no archival or literature reviews, field surveys, or Native American consultations have been conducted for the Proposed Action Alternative APE.  Nevertheless, based on the governing PA, actions such as the replacement and disposal of ties, cleaning drainage ditches, replacing ballast, and replacing damaged drainage culverts (where the work is substantially in-kind and the surrounding structures are not of historic significance) in previously disturbed areas would not require further review by the SHPO.  Repair of traffic control devices (such as signals) using in-kind systems and the procurement of materials and equipment would also not require further SHPO review.  These activities comprise the majority of the proposed actions for the project.

Structural upgrades, such as bridges, and any activities undertaken outside of the existing alignment in undisturbed areas, such as construction of staging sites, may require further review depending on their specific location and footprint.  For these actions, NCRA must evaluate the action based on the criteria set forth in Appendix 1 of the PA to determine whether further SHPO consultation is necessary.  NCRA would conduct appropriate archival, field surveys and Native American consultation on behalf of FEMA in order to help satisfy FEMAs Section 106 compliance responsibilities.  FEMA would then conduct formal consultation with the SHPO.  Any additional actions precipitated by this consultation would be the responsibility of NCRA to complete (for example, site evaluations and subsequent treatment or mitigation). 

All activities to be undertaken as part of the Proposed Action Alternative are subject to the provisions of the PA.  In the event of an unanticipated discovery during any activity supported by FEMA, the NCRA would stop work and notify FEMA immediately.  FEMA would then consult with the SHPO in accordance with Section VII of the PA.  Should human remains be encountered, work in the vicinity would halt and the NCRA would notify the County Coroner immediately.  If the remains were determined to be Native American, the coroner would contact the Native American Heritage Commission.
3.7 	Socioeconomics 
3.7.1 	Affected Environment
The regulatory framework and affected environment are described in Section 3.8 of the Flood PEA.  For the South End Railroad project, the study area covers portions of Mendocino, Sonoma, and Marin counties.  At its southeastern end, the railroad also crosses a 12-mile distance through Napa County, connecting the NWP line to the Union Pacific mainline at Fairfield-Suisun in Solano County.  Although the railroad crosses four county lines, its impact in Napa County is limited given the small area of the county that is affected by the project.

According to the 2000 Census data, Mendocino County has an estimated population of 86,265, a growth of 7.4 percent from 1990.  The top employers by industry are professional services (nearly 30 percent), sales and office occupations (23 percent), and other service jobs (19.5 percent).  The per capita income in the county in 2000 was $19,443 and the median household income was $35,996, while the unemployment rate for the county was 4.5 percent and 15.9 percent of the population fell below the poverty level.  During that time, the median home price in Mendocino County was $170,200.

Sonoma County experienced the highest population growth in the area  up to 458,614 in 2000 from 388,222 in 1990 (an 18 percent increase).  As in Mendocino County, the top employer was the professional services industry (35 percent, followed by sales and office occupations (26.6 percent).  In addition, other services employed nearly 15 percent of the workforce.  The unemployment rate in 2000 was 2.8 percent, and 8.1 percent of the population was below the poverty line.  The per capita income was $25,724 and the median household income was $53,076.  The median home price in the County was $273,200.
Marin County had a population of 247,289 in 2000, a growth of 7.5 percent from 1990.  Among the counties in the study area, Marin County had the highest income with a per capita income of $44,962 and a median household income of $71,306.  Over 20 percent of the labor force was employed in the professional services industry, followed by over 18 percent in the educational services sector.  Only 6.6 percent of individuals were recorded as being below the poverty line and the unemployment rate was 1.9 percent.  The median home price in 2000 was $514,600.

Napa County had a population of 124,279, a per capita income of $26,395, and a median household income of $51,738 in 2000.  Over 80 percent of the population was White, with the Hispanic group representing the largest ethnic minority.  Only 8.3 percent of individuals in Napa and County fell below the poverty line in 2000.
3.7.2 	No Action Alternative
Impacts of the No Action Alternative are described in Section 4.1.8.1 of the Flood PEA.  If no action is taken to restore the function of the freight railroad, the region would suffer an adverse economic impact.  The freight railroad provides a commercial service, transporting goods from one area to another.  Without this service, goods are moved in trucks on Highway 101. 
3.7.3 	Proposed Action Alternative
Impacts of Proposed Action Alternative are described in Section 4.1.8.3 of the Flood PEA.  Since the railroad operated prior to the 1997-1998 flood event, rehabilitating the South End Railroad through the implementation of the proposed actions would ultimately lead to beneficial impacts on socioeconomic resources.  Damaged facilities would be restored, decreasing hazards to people associated with the railroad facilities.  With the eventual restoration of freight service, other benefits to the community may also be realized. These benefits would be associated with the operation of the railroad, and would be addressed separately by NCRA.
In compliance with Executive Order 12898 (Environmental Justice), FEMA determined that neither the implementation of the No Action Alternative nor the Proposed Action Alternative is expected to result in any adverse and/or disproportionate impacts on minority or low-income persons.
3.8	Land Use and Zoning
3.8.1	Affected Environment
The affected environment is described in Section 3.9 of the Flood PEA.  The NWP is a pre-existing railroad.  As such, NCRA owns the right-of-way along its route.  No work is proposed outside NCRAs existing right-of-way.  

3.8.2	No Action Alternative
Impacts of the No Action Alternative are described in Sections 4.1.9.1 of the Flood PEA.  Because no new structures would be built outside NCRAs right-of-way, the No Action Alternative would not affect land use or zoning. 
3.8.3	Proposed Action Alternative
Impacts of the Proposed Action Alternative are described in Section 4.1.9.3 of the Flood PEA. No impact to land use or zoning would result from the Proposed Action Alternative.  All project activities would occur within NCRAs existing right-of-way.
3.9    	Public Services

3.9.1 Affected Environment

The affected environment is described in Section 3.10 of the Flood PEA.  Public services include fire protection, police protection, public schools, parks, and other services at public facilities. Guidelines and statutes regarding public services are generally found at the local level.  Local jurisdictions frequently establish building codes and other construction standards and prescribe requirements for local police and fire protection. Local planning agencies may establish goals or ordinances for parks or keeping areas undeveloped. Although state and the federal government constrain aspects of school policy decision making, local school boards determine school operations. 

3.9.2 No Action Alternative

Impacts of the No Action Alternative are described in Section 4.1.10.1 of the Flood PEA.  Under the No Action Alternative, no improvements would be made to the railroad and no public services would be affected. 

3.9.3 Proposed Action Alternative

Impacts of the Proposed Action Alternative are described in Section 4.1.10.3 of the Flood PEA.  No impacts to public services are expected to result from the restoration and upgrading of the railroad facilities.  All proposed actions are within the railroad right-of-way, where the railroad previously operated.  Any temporary impacts that could restrict the access of emergency services in the study area will be avoided. Mitigation measures to avoid temporary impacts to public services may include timing construction activities to minimize impacts to public utility users.  NCRA would be responsible for implementing such measures.





3.10 Transportation

3.10.1 Affected Environment

The affected environment is described in Section 3.11 of the Flood PEA.  The study area is located alongside Highway 101 for much of its length.  


3.10.2 No Action Alternative

Impacts of the No Action Alternative are described in Section 4.1.11.1 of the Flood PEA.  Under the No Action Alternative, FEMA would not assist with actions that would repair and improve the railroad; therefore, benefits to transportation would not be realized. Without the proposed actions, the railroad would not become operational and future disaster events have the potential to cause additional damage.


3.10.3 Proposed Action Alternative

Impacts of the Proposed Action Alternative are described in Section 4.1.11.3 of the Flood PEA.  In general, the implementation of the proposed actions may result in some temporary, minor impacts to transportation. To minimize adverse impacts to traffic and circulation, NCRA would be required to implement the following mitigation measures or more stringent measures, if so required by local law or ordinance:

* Traffic along adjacent roadways would be temporarily rerouted as necessary during construction activities. Traffic lane closures would be coordinated with appropriate community officials.

* To the maximum extent feasible, construction-related vehicles would be prohibited from parking on residential streets.

* Construction equipment and vehicle staging would be located to hinder the traffic flow as little as possible in the areas where the actions are implemented.

Adjacent residential neighborhoods and commercial/industrial areas would be notified in advance of construction activities and any rerouting of local traffic. Notification would identify a local contact.

3.11	Noise

3.11.1	Affected Environment

The affected environment and regulatory background is described in Section 3.12 of the Flood PEA. 


3.11.2 No Action Alternative

Impacts of the No Action Alternative are described in Section 4.1.12.1 of the Flood PEA. Under the No Action Alternative, no permanent changes to noise levels are expected because the railroad would remain non-operational. 

3.11.3 Proposed Action Alternative

Impacts of the Proposed Action Alternative are described in Section 4.1.12.3 of the Flood PEA.  Construction activities would typically result in temporary noise from construction equipment. Construction activities would comply with local noise ordinances and state and federal standards and guidelines. Special precautions may be required around noise-sensitive receptors such as funeral homes, schools, or hospitals. These precautions, which would be implemented by NCRA, may include special work hours or public notification.
NCRA would comply with local noise ordinances and state and federal standards and guidelines for potential impacts caused by constructing noise-generating facilities.


3.12	Hazardous Materials and Wastes

3.12.1	Affected Environment

The affected environment is described in Section 3.13 of the Flood PEA.  Hazardous materials and wastes are grouped into the following four categories based on their properties: toxic (causes human health effects), ignitable (has the ability to burn), corrosive (causes severe burns or damage to materials), and reactive (causes explosions or generates toxic gases) (CCR Title 22, Division 4.5, Chapter 11, Article 3). Although petroleum products are not considered a hazardous material under federal regulations, they are regulated as hazardous materials in California.

A hazardous material is defined in many ways according to different federal and state regulations. In California, hazardous material is defined as:

* Any substance designated pursuant to the Clean Water Act (CWA) Section 311(b)(2)(A), as amended (33 USC Section 466 et seq.);

* Any element, compound, mixture, solution, or substance designated pursuant to the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) Section 102, as amended (42 USC Section 9601 et seq.);

* Any substance as defined by the California Health and Safety Code, Chapter 6.5, Hazardous Waste Control;

* Any toxic pollutant listed under CWA Section 307(a), as amended (33 USC Section 466 et seq.);

* Any hazardous air pollutant listed under the Clean Air Act (CAA) Section 112, as amended (42 USC Section 1857 et seq.); and

* Any imminently hazardous chemical substance or mixture with respect to which the USEPA has taken action pursuant to Toxic Substance Control Act Section 7, as amended (15 USC Section 2601 et seq.).

A hazardous material in California includes petroleum, natural gas, natural gas liquids, liquefied natural gas, or synthetic gas usable for fuel. A hazardous waste is any hazardous material that is discarded, abandoned, or transported and stored prior to being recycled. The criteria that render a material hazardous also make a waste hazardous.  Hazardous materials and wastes can result in public health hazards if released to the soil or groundwater or through airborne releases in vapors, fumes, or dust. Hazardous wastes must be disposed of in accordance with all federal and California hazardous waste regulations.

Hazardous materials and wastes are likely to be part of the affected environment of the South End Railroad project. In general, actions that are foreseen to involve hazardous materials or wastes include demolition or modification of:

* Replaced ballasts;

* Replaced creosote-coated railroad ties; and

* Removed debris that may contain chemical or other potentially hazardous materials

3.12.2	No Action Alternative

Impacts of the No Action Alternative are described in Section 4.1.13.1 of the Flood PEA.  Hazardous materials and wastes are not expected to be present in the study area because the project does not involve the transport, use, or disposal of hazardous materials or wastes and would not result in creation of a public health hazard.  However, some contamination in the debris at or around the project site may exist. 

3.12.3 Proposed Action Alternative

Impacts of Proposed Action Alternative are described in Section 4.1.13.3 of the Flood PEA.  The restoration of exiting facilities is not expected to directly impact hazardous materials and wastes.  In general, hazardous materials at the sites of potential actions (for example, underground storage tanks [USTs] and toxic release sites) would not be altered from their existing condition under this action. In circumstances where hazardous materials and wastes are involved in restoration activities, public or private entities responsible for restoration are expected to follow all applicable local, state, and federal regulations for use, storage, handling, and disposal of these substances.

Specific activities may disturb hazardous materials present at the site of an action. NCRA would conduct a site assessment (such as a Phase I Environmental Site Assessment) to determine if such materials are present. USTs would also be identified as part of this study.  NCRA would follow local, state, and federal regulations for the handling and disposal of hazardous materials or for removing USTs.  NCRA would coordinate with the Air Quality Management District, State Water Resources Control Board, California Air Resources Board, and the USEPA, as appropriate.  For example, the disposal, recycling, or replacement of railroad ties and ballast materials would require the use of gloves as hazardous materials like creosote could be present.  The removal and proper disposal of the materials would result in a beneficial effect to the community.




4.0	CUMULATIVE IMPACTS

In 1999, the California Department of Fish and Game (CDFG), Department of Toxic Substances Control, North Coast Regional Water Quality Control Board and the NCRA entered into a Consent Decree in an effort to resolve claims in a complaint alleging violations of the Fish and Game Code, Health and Safety Code, and Water Code.  The Consent Decree requires that NCRA and its contract operators perform corrective actions and adhere to prescribed environmental management practices along both the northern and southern portions of the NWP in order to provide appropriate injunctive relief.  

By providing funding for the South End Railroad project as an alternate project, FEMA funds for the northern portion of the NWP would become unavailable.  Nevertheless, NCRA will continue to be responsible for full compliance with the Consent Decree.  Actions undertaken along the northern portion of the NWP would also contribute to cumulative environmental effects in the study area.

While individual actions taken as part of the South End Railroad project would likely be completed prior to the earliest anticipated activity of the SMART commuter rail project (Section 1.2.1), there are likely to be cumulative effects associated with the development of the SMART project.  These impacts would be described in the environmental documentation for the SMART passenger rail service.  Resource areas in which cumulative impacts may occur include air quality, biological resources, socioeconomics, transportation, and noise. 

Resumption of freight service along the railroad would have additional cumulative environmental effects not addressed in this document.  Actions taken to resume operations that are above and beyond those described in the South End Railroad project would be evaluated separately by NCRA.  Resource areas that would be affected by the operation of the railroad include air quality, noise, traffic / transportation, public safety, biological resources, and socioeconomics.  

Detailed cumulative impacts are not addressed in this South End Railroad PEA because analysis of these impacts requires specific knowledge of actions occurring or proposed by SMART to occur within or near the study area.


5.0	REFERENCES
		
California Air Resources Board (CARB). 2003. Ambient air quality standards. URL: http://www.arb.ca.gov/aqs/aaqs2.pdf. California Environmental Protection Agency, Sacramento, CA. 

California Department of Water Resources. n.d. World Wide Web home pages (links to the four California groundwater districts). Website located at http://www.dwr.water.ca.gov/about/websites.html. Sacramento, CA.

California Natural Diversity Data Base (CNDDB).  2003. California Natural Diversity Data Base. Rarefind database. California Department of Fish and Game. April 9, 2003 version.

California Natural Resources (CNR).  2003.  Website located at
http://ceres.ca.gov/ceres/calweb/coastal/plants/smarsh.html.

California Department of Fish and Game (CDFG).  2003.  Website located at http://www.dfg.ca.gov/hcpb/species/t_e_spp/tespp.shtml.

Chaty, Dennis.  Planner, County of Mendocino Planning and Building Services.  Personal communication with M. Kothari, URS on 9/18/2003.

CNPS Letter.  2003.  California Vernal Pool Preliminary Report.
URL: http://www.cnpsmb.org/pdfs/021303_cac.pdf.

FEMA 1998. Final Programmatic Environmental Assessment for Typical Recurring Actions Resulting from Flood Disasters in California as Proposed by the Federal Emergency Management Agency. April 16, 1998. FEMA 1203-DR-CA.

Mendocino County.  2003.  Ukiah Valley Area Plan.  March 18.  Website at http://www.co.mendocino.ca.us/planning/UVAP/031803/BOSUVAPIndex.htm.

National Marine Fisheries Service (NMFS).  2003.  URL: http://www.nmfs.noaa.gov/.

U.S. Census Bureau. 1990 and 2000 statistics. URL: http://factfinder.census.gov.

U.S. Fish and Wildlife Service (USFWS).  2002.  Website located at http://sacramento.fws.gov/es/animal_spp_acct/california_tiger_salamander.htm.

Wakabayashi, J., and Smith, D.L. 1994. Evaluation of recurrence intervals, characteristic earthquakes and slip-rates associated with thrusting along the Coast Range-Central Valley geomorphic boundary. Bulletin of the Seismological Society of America 84:1960-1970.

Watkin, Jim.  1999.  Wildlife Biologist, U.S. Fish and Wildlife Service.  Personal communication with Kristin Byrd, URS Corporation.

Wetland Campaign.  2003. 
      URL: http://www.audubonsfbay.org/sfbay_2_16/whatwedo_bay_map10.html

Wicks, C.W., Thatcher, W., Monastero, F.C., and Hasting, M.A. 2001. Steady state deformation of the Coso Range, east central California, inferred from satellite radar interferometry. Journal of Geophysical Research 106:13,769-13,780.

Youd, T.L., and Hoose, S.N. 1978. Historical ground failures in Northern California triggered by earthquakes. U.S. Geological Survey Professional Paper 993.


Figures











Appendix A  NCRA Application for Alternate Project 





	

















Appendix B  Species Table

 

To prepare this table, species information was obtained from the U.S. Fish and Wildlife Service for the geographic area covered by the following U.S. Geological Survey 7.5-minute quadrangle maps:  Burbeck, Willits, Laughlin Range, Redwood Valley, Orrs Springs, Ukiah, Elledge Peak, Purdys Gardens, Yorkville, Hopland, Cloverdale, Asti, Geyserville, Jimtown, Guerneville, Healdsburg, Mark West Springs, Sebastopol, Santa Rosa, Two Rock, Cotati, Glen Ellen, Petaluma, Petaluma River, Novato, Petaluma Point, and Sears Point.

Legend: E = federally listed as endangered; T = federally listed as threatened; PT = federally proposed threatened; C = candidate

Scientific Name
Common Name
Federal Status
Preferred Habitat
Likelihood of Occurring in the Study Area
Amphibian




Ambystoma californiense
California tiger salamander
PT
Annual grasslands and grassy understory of valley-foothill hardwood habitats, need underground refuges, need vernal pools, meadows, seeps, stock ponds or other seasonal water resources for breeding. This species occurs from near Petaluma (Sonoma County) east through the Central Valley to Yolo and Sacramento Counties and south to Tulare County, and from the vicinity of San Francisco Bay south at least to Santa Barbara County.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is near the alignment.
Bufo canorus
Yosemite toad
C
Small montane toad, endemic to the Sierra Nevada Mountains from Ebbetts Pass, Alpine County to south of Kaiser Pass and Evolution Lake, Fresno County. Species occurs from 6,400 to 11,300 feet elevation, with the majority of sites between 8,500 and 10,000 feet; found in open montane meadows near lodgepole pine forests.
No potential to occur within the study area given the species elevation requirements and species range.
Rana aurora draytonii
California red-legged frog
T
Dense, shrubby riparian vegetation associated with deep (> 0.7 m), still or slow-moving water.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 0.3 miles from the study area.

Scientific Name
Common Name
Federal Status
Preferred Habitat
Likelihood of Occurring in the Study Area
Birds




Brachyramphus marmoratus
Marbled murrelet
T
Occurs year-round in marine subtidal and pelagic habitats from Oregon border to Point Sal, Santa Barbara County. In summer forages close to shore; in nonbreeding season forages farther from shore. Breeders require mature, coastal coniferous forest for nesting and nearby coastal waters for feeding.
Potential to occur if suitable habitat exists within the study area.
Critical habitat is found in four USGS quadrangles in the study area.
Charadrius alexandrinus nivosus
Western snowy plover
T
Habitats used by nesting and non-nesting birds include sandy coastal beaches, salt pans, coastal dredged spoil sites, dry salt ponds, salt pond levees and gravel bars.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 1.7 miles from the study area.
Coccyzus americanus
Western yellow-billed cuckoo
C
Inhabits extensive deciduous riparian thickets or forests with dense, low-level or understory foliage, and which abut on slow-moving watercourses, backwaters, or seeps.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 1 mile from the study area.
Haliaeetus leucocephalus
Bald eagle
T
Winters throughout most of California at lakes, reservoirs, river systems, and some rangelands and coastal wetlands on protected cliffs and ledges. Also nests on bridges and buildings in urban areas. Nests are normally built in the upper canopy of large trees, usually conifers.
Potential to occur if suitable habitat exists within the study area.
Pelecanus occidentalis californicus
California brown pelican
E
Found in estuarine, marine subtidal, and marine pelagic waters along the California coast. In northern California, fairly common to common June to November. Usually rests on water or inaccessible rocks (either offshore or on mainland), but also uses mudflats, sandy beaches, wharfs, and jetties.
Not likely to occur because study area lacks suitable habitat.
Rallus longirostris obsoletus
California clapper rail
E
Tidal salt marshes near tidal sloughs; perennial inhabitant of tidal salt marshes of the greater San Francisco Bay.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is near the alignment.
Sterna antillarum (=albifrons) browni
California least tern
E
Nests in flat, open areas along the coast near inshore estuaries, river mouths, or shallows, sandy ground with little or no vegetation, bays, freshwater ponds, channels, lakes.  
Not likely to occur within the study area. 
Strix occidentalis caurina
Northern spotted owl
T
Old-growth forests or mixed stands of old-growth and mature trees; occasionally in younger forests with patches of big trees. Ranges through the Cascade and Sierra Nevada mountains, primarily on the west slope, from Shasta County south to Kern County, Tehachapi Range, and the mountains of southern CA.
Potential to occur if suitable habitat exists within the study area.
Critical habitat is found in two USGS quadrangles surrounding Willits.
Mammals




Reithrodontomys raviventris
Salt marsh harvest mouse
E
Coastal salt marsh, dense stands of pickleweed.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 300 feet from the study area.
Fish




Acipenser medirostris
Green sturgeon
C
A demersal (bottom dwelling) species, mostly seen from inshore waters to 60 m (197 feet). Spawn in the main stem of large river systems in relatively fast water flows and probably in depths greater than 3 m. Preferred spawning substrate is large cobble, but can range from clean sand to bedrock. Spawning has been confirmed in recent years only in the Sacramento River and the Klamath River, although spawning probably once occurred in the Eel River as well.
Potential to occur if suitable habitat exists within the study area.

Eucyclogobius newberryi
Tidewater goby
E
Brackish shallow lagoons and lower stream reaches where the water is fairly still but not stagnant; found in water with salinity levels from zero to 10 ppt, temperature levels from 35 to 73 degrees Fahrenheit, and water depths from 5 to 7.5 feet. Historically, this species occurred in coastal lagoons from San Diego County to Humboldt County, but it has disappeared from most of these sites.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is near the alignment.
Hypomesus transpacificus 
Delta smelt 
T
Euryhaline species, but for a large part of its life span, it is associated with the freshwater edge of the mixing zone (saltwater-freshwater interface). Spawning habitats are side channels and sloughs in the middle reaches of the Delta. Spawn in shallow freshwater from December through July (Goals Project, 2000). Pelagic feeder. This species occurs only in Suisun Bay and the Sacramento-San Joaquin estuary (known as the Delta) near San Francisco Bay Area.
Unlikely to occur.  Would only occur as strays.
Oncorhynchus mykiss
Central Valley steelhead 
T
Pacific Ocean, spawns in coastal streams and rivers, over gravel beds. Pool depth, volume, amount of cover, and proximity to gravel for spawning play key roles.
Unlikely to occur.  This ESU is defined outside of the study area, but is located within a 5-mile radius of the alignment.
Oncorhynchus mykiss
Central California coast steelhead
T
Pacific Ocean, spawns in coastal streams and rivers, over gravel beds. Pool depth, volume, amount of cover, and proximity to gravel for spawning play key roles.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is approximately 0.4 miles from study area.
Oncorhynchus mykiss
Northern California steelhead
T
Pacific Ocean, spawns in coastal streams and rivers, over gravel beds. Pool depth, volume, amount of cover, and proximity to gravel for spawning play key roles.
Potential to occur if suitable habitat exists within the study area.
Oncorhynchus kisutch
Central California coast coho salmon
T
Pacific Ocean, spawns in coastal streams and rivers, over gravel beds. Pool depth, volume, amount of cover, and proximity to gravel for spawning play key roles.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is approximately 0.4 miles from study area located in the Russian River at Hwy 101 bridge in Healdsburg.
Oncorhynchus kisutch
Southern Oregon / Northern California coho salmon
T
Pacific Ocean, spawns in coastal streams and rivers, over gravel beds. Pool depth, volume, amount of cover, and proximity to gravel for spawning play key roles.
Potential to occur if suitable habitat exists within the study area.
Oncorhynchus tshawytscha
California coastal chinook salmon
T
Pacific Ocean, spawns in coastal streams and rivers, over gravel beds. Pool depth, volume, amount of cover, and proximity to gravel for spawning play key roles.
Potential to occur if suitable habitat exists within the study area.
Oncorhynchus tshawytscha
Central Valley spring-run chinook salmon
T
Pacific Ocean, spawns in coastal streams and rivers, over gravel beds. Pool depth, volume, amount of cover, and proximity to gravel for spawning play key roles.  Spring-run chinook salmon are primarily found in four tributaries to the Sacramento River (Butte, Big Chico, Deer, and Mill creeks), but there are other waters that may contain them.
Unlikely to occur.  This species is primarily found in the Sacramento River.  Therefore, it occurs outside of the study area, but it is located within a 5-mile radius of the alignment.
Oncorhynchus tshawytscha
Central Valley fall/late fall-run chinook salmon
C
Pacific Ocean, spawns in coastal streams and rivers, over gravel beds. Pool depth, volume, amount of cover, and proximity to gravel for spawning play key roles. Found mainly in the Sacramento River, and most spawning and rearing of juveniles takes place in the reach between Red Bluff and Redding.
Unlikely to occur.  This species is primarily found in the Sacramento River.  Therefore, it occurs outside of the study area, but it is located within a 5-mile radius of the alignment.
Pogonichthlys macrolepidotus
Sacramento splittail
T
Euryhaline species, but prefers freshwater. Primarily found in backwater sloughs of the Sacramento-San Joaquin Delta and Suisun Marsh. They are now largely confined to: (1) the Delta, (2) Suisun Bay, (3) Suisun Marsh, (4) Napa River, (5) Petaluma River, and (6) other parts of the Sacramento-San Joaquin Estuary.  Upstream spawning migration occurs from November through May into freshwater habitats (Goals Project 2000).
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is near the alignment.
Invertebrates




Branchinecta lynchi
Vernal pool fairy shrimp
T
Vernal pools; small swales, earth slumps, or basalt-flow depression basins with grassy or occassionally muddy bottom, in unplowed grassland (Eriksen and Belk 1999).
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 1.3 miles from the study area.
Speyeria callippe callippe
Callippe silverspot butterfly
E
Coastal scrub. Host plant is violet, including Viola purpurea, V. pedunculata, V. beckwithii, V. douglasii, and V. nuttalli
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 1 mile from the study area.
Speyeria zerene myrtleae
Myrtles silverspot butterfly
E
Restricted to areas immediately adjacent to the coast, such as dunes, scrub, and grasslands. The eggs are laid only on species of Viola, possibly only Viola adunca. This species is only known from a few sites in northern Marin County.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 1 mile from the study area.  This occurrence is located west of Sears Point, approximately 2 miles north of the junction of Lakeville Hwy and Black Point Road.
Syncaris pacifica
California freshwater shrimp
E
Small, perennial coastal streams. Excellent habitat conditions include: streams of 12 to 36 inches in depth, with exposed live roots of trees such as alder and willow, along undercut banks greater than 6 inches, with overhanging overhanging woody debris or stream vegetation and vines such as stinging nettles, grasses, vine maple and mint. 
Historically, this shrimp was probably common in low elevation, perennial freshwater streams in Marin, Sonoma, and Napa counties. Today, it is found in sixteen stream segments within these counties, in four general geographic regions: 1) tributary streams in the lower Russian River drainage, which flows westward into the Pacific Ocean; 2) coastal streams flowing westward directly into the Pacific Ocean; 3) streams draining into Tomales Bay; and, 4) streams flowing southward into northern San Pablo Bay. 
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 0.5 miles from the study area.
Plants




Alopecurus aequalis var. sonomensis
Sonoma alopecurus
E
Freshwater marshes and swamps; riparian scrub.  The blooming period extends from May through July.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 2 miles from the study area.
Astragalus clarianus
Clara Hunts milk-vetch
E
Chaparral, cismontane woodland, valley and foothill grassland; grows in serpentinite or volcanic, rocky, clay. 
Potential to occur if suitable habitat exists within the study area.
Blennosperma bakeri
Bakers stickyseed
E
Valley and foothill grassland; vernal pools. The blooming period extends from March through May.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 0.3 miles from the study area.
Carex albida
White sedge
E
Meadows and seeps; freshwater marshes and swamps. The blooming period extends from May through July.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is near the alignment.
Chorizanthe valida
Sonoma spineflower
E
Coastal prairie. The blooming period extends from June through August.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is near the alignment.
Clarkia imbricata
Vine Hill clarkia
E
Chaparral, valley and foothill grassland. The blooming period extends from June through August.
Potential to occur if suitable habitat exists within the study area.
Cordylanthus mollis ssp. mollis
Soft birds beak
E
Coastal salt marshes and swamps. The blooming period extends from July through November.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 0.4 miles from the study area.
Cordylanthus tenuis ssp. capillaris
Pennells birds-beak
E
Coniferous forest, chaparral; serpentinite. The blooming period extends from June through September.
Potential to occur if suitable habitat exists within the study area.
Delphinium bakeri
Bakers larkspur
E
Coastal scrub, valley and foothill grassland. The blooming period extends from March through May.
Potential to occur if suitable habitat exists within the study area.
Critical habitat has been proposed (but not designated) in the Petaluma USGS quadrangle.
Delphinium luteum
Yellow larkspur
E
Chaparral, coastal prairie, coastal scrub. The blooming period extends from March through March.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 0.7 miles from the study area.
Hesperolinon congestum
Marin dwarf-flax (=western flax)
T
Chaparral, valley and foothill grassland; serpentinite. The blooming period extends from April through July.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 1.4 miles from the study area.
Lasthenia burkei
Burkes goldfields
E
Meadows and seeps; vernal pools. The blooming period extends from April through June.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is near the alignment.
Lasthenia conjugens
Contra Costa goldfields
E
Cismontane woodland, alkaline playas, valley and foothill grasslands, and vernal pools. The blooming period extends from March through June.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 1 mile from the study area.
Lilium pardalinum ssp. pitkinense
Pitkin Marsh lily
E
Cismontane woodland, meadows and seeps, freshwater marshes and swamps. The blooming period extends from June through July.
Potential to occur if suitable habitat exists within the study area.
Limnanthes vinculans
Sebastopol meadowfoam
E
Wetlands, meadows and seeps, valley and foothill grasslands, and vernal pools. The blooming period extends from April through May.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 0.3 miles from the study area.
Navarretia leucocephala ssp. plieantha
Many-flowered navarretia
E
Vernal pools. The blooming period extends from May through June.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 0.9 miles from the study area.
Potentilla hickmanii
Hickmans potentilla (=cinquefoil)
E
Coastal bluff scrub, closed-cone coniferous forest, meadows and seeps, freshwater marshes and swamps. The blooming period extends from April through August.

Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 4.5 miles from the study area.
Trifolium amoenum
Showy Indian clover
E
Coastal bluff scrub, valley and foothill grassland; sometimes serpentinite. The blooming period extends from April through June.
Potential to occur if suitable habitat exists within the study area.  Closest known occurrence is located approximately 0.2 miles from the study area.

       Source: USFWS species lists for 27 USGS quadrangles and a CNDDB search surrounding the railroad alignment using 5-mile radius.	







DRAFT Programmatic Environmental Assessment 		Federal Emergency Management Agency
November 2003		Page 2



DRAFT Programmatic Environmental Assessment 		Federal Emergency Management Agency
October 2003		Page 37



Table 1:  Federally Listed, Proposed, and Candidate Species 
With Potential to Occur in the Vicinity of the North Coast Railroad Project

DRAFT Programmatic Environmental Assessment
Appendix B  Page 11