Upper Berryessa Creek Flood Risk Management Project, Santa Clara County, California : Final Environmental Impact Report

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by  Tetra Tech, Inc., Santa Clara Valley Water District.

Upper Berryessa Creek Flood Risk Management Project
Santa Clara County, California

Final Environmental Impact Report
(State Clearinghouse No. 2001104013)

January 2016

Prepared for:

Prepared by:
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EXECUTIVE SUMMARY

ES.1 INTRODUCTION
This document addresses proposed modifications to Upper Berryessa Creek within the cities of Milpitas
and San Jose, California. These modifications include flood risk management improvements along
2.2 miles of Upper Berryessa Creek, stretching from I-680 downstream to Calaveras Boulevard. The
primary improvements include:
• Constructing a floodwall at the area identified as being most in danger of overtopping;
• Excavating sediment and vegetation;
• Enhancing flood passage through culverts and bridges; and
• Improving access for maintenance, including sediment removal and vegetation management.

As the primary water resources agency for Santa Clara County (the County), the Santa Clara Valley
Water District (the District) provides water-related services including wholesale distribution, stream
maintenance, and flood protection throughout the Santa Clara Valley. In order to alleviate flooding in
the Upper Berryessa Creek area, the District is proposing flood risk management measures that would
provide protection from the base flood (also referred to as the 100-year flood).

The District has formed a partnership with the U.S. Army Corps of Engineers (USACE) to plan and
implement the proposed project. The USACE is the Federal project sponsor and the District is the local
sponsor. USACE would be responsible for permitting, contracting and oversight of construction activities
and the District would be responsible for acquiring real property needed for the project (including
temporary and permanent easements), making real property owned or to be acquired by the District for
the project available for construction, and operating and maintaining the creek channel after
construction is complete.

As part of the process of studying the feasibility of the proposed project and its alternatives, the USACE
prepared the Berryessa Creek Integrated General Reevaluation Report (GRR) and Environmental Impact
Statement (EIS), which was finalized in 2014. The GRR/EIS documents the planning and evaluation
process that identified the USACE’s preferred alternative, the results of hydraulic, economic,
geotechnical, and other studies that informed the process, and the environmental impacts that could
occur during construction and operation of the proposed project. As the GRR/EIS has been finalized, the
USACE is preparing the project designs and intends to implement the selected plan. The District’s
proposed project consists of the project as selected by the USACE with an improvement that would
increase the level of flood protection to meet Federal Emergency Management Agency (FEMA)
certification standards. The improvement that would be added to the USACE-selected project to achieve
FEMA certification is increasing the length and height of a concrete floodwall located on the west bank
of the creek in Reaches 2 and 3. The USACE-selected project design includes a roughly 1,300 foot long,
1.5 foot high floodwall at this location; the proposed project would increase the length of the floodwall
to about 2,200 feet. The maximum height of the floodwall would be 2 feet above ground level.

The District determined that construction of the proposed project could have a significant effect on the
environment and is has therefore prepareding this Environmental Impact Report (EIR) in compliance
with the California Environmental Quality Act (CEQA). This Draft EIR (DEIR) is intended to:
• Provide a complete description of the proposed project to the public;
• Inform the public of any significant impacts that could occur as a result of project
implementation;
• Identify measures that would avoid, reduce, or mitigate any significant effects; and
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• Describe and evaluate other alternatives that may feasibly accomplish the goals and objectives
of the proposed project.

ES.2 OBJECTIVES
The District developed three project-specific objectives, which provide the basis for potential
modifications to complete the proposed project.

Objective 1: Reduce flood damages from Berryessa Creek upstream of Calaveras Boulevard throughout
the study reach during the 50-year period of analysis beginning in 2017. Completed project would meet
FEMA certification standards in all 4 project reaches.

Objective 2: Use environmentally sustainable design practices in addressing the flood risk management
purpose of the project wherever possible within the study reach, including taking advantage of
restoration opportunities that may be pursued incidentally to the flood damage reduction purpose.

Objective 3: Be consistent with Berryessa Creek Flood Risk Management Project Plan selected by USACE
in the Director’s Report of May 29, 2014.

ES.3 BACKGROUND
Flooding within the Berryessa Creek watershed and vicinity has occurred often during the past decades.
Stormwater flooding that inundates streets and yards occurs an average of at least once every 4 years.
Overflow channel flooding also occurs along Upper Berryessa Creek on average of once every 10 to 20
years, which results in significant damage to homes, businesses, infrastructure, and automobiles.

High rainfall events occurring in 1982, 1983, and 1998 caused extensive flooding and damage to areas
along creeks in the cities of San Jose and Milpitas. As a result of these and other floods, the District and
the USACE commenced studies to identify areas of Berryessa Creek and its tributaries, a part of the
Coyote Watershed, that are most vulnerable to flooding. Teams of hydraulic engineers, planners, and
field inspectors reviewed historic flood information, topographic maps, and other available data and
reports, and prepared detailed hydraulic models of the Upper Berryessa Creek system. The resulting
studies in hydraulics, economics, geotechnical issues, hazardous materials, and sediment movement
resulted in the Berryessa Creek Project GRR-EIS. These studies indicate that Upper Berryessa Creek does
not have sufficient capacity to contain the 1 percent (100-year) recurrence flood, meaning that
destructive flooding would continue to occur unless measures are taken to expand flow capacity. The
dollar value of flood damage from the 1 percent flood is estimated at $528 million in 2011 dollars
(USACE 2014).

ES.4 PROJECT SUMMARY
Working closely with USACE, the District has developed the Upper Berryessa Creek Flood Risk
Management Project, which is described and analyzed in this EIR. The proposed project would provide
flood protection and flood damage reduction benefits along Upper Berryessa Creek by incorporating
channel, bridge, and top of bank improvements designed to convey the 1 percent recurrence flood
within its banks. The proposed project consists of the USACE-selected project with addition of a taller
and longer concrete floodwall in Reaches 2 and 3 compared to the USACE-selected project. The
proposed project is designed to meet FEMA certification standards. The proposed project would remove
an estimated 500 parcels of land from the flood hazard zone. Under the proposed project, all work
would occur downstream of I-680 and upstream of Calaveras Boulevard. The District is implementing a
separate project to improve the flow conveyance capacity of Lower Berryessa Creek between Calaveras
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Boulevard and the Lower Penitencia Creek confluence. Calaveras Boulevard forms the boundary
between the Upper Berryessa Creek Flood Risk Management Project and the Lower Berryessa Creek
Flood Protection Improvements Project. Both projects would be designed to contain the 1 percent flow
without overtopping of banks. The channel of Upper Berryessa Creek would be designed with vegetated
side walls to add capacity and provide bank protection within the existing right-of-way (ROW). The
channel banks would be protected with biodegradable erosion control blankets and hydroseeded, an
approach that has been shown in the Design Documentation Report (Tetra Tech 2015f) to be sufficient
to prevent significant erosion. The channel would also have an earthen channel bottom with buried rock
revetments for channel stability. The existing access road alignments would be retained and additional
access added on the east bank at the downstream end of the project area.

ES.5 CONSTRUCTION AND MAINTENANCE
Construction of the proposed project would include excavating a wider channel, constructing a floodwall
on the west bank, installing a concrete box culvert to replace an existing railroad trestle as well as
installing new culverts at the mouths of Piedmont and Los Coches Creeks, revegetating affected areas,
and constructing or upgrading access roads. Construction would occur over 1 to 2 years, with
construction primarily occurring between May and October to coincide with the driest time of year.
Construction hours would generally be during normal business hours, but after-hours work may be
needed to pour concrete or replace the existing UPRR trestle with a concrete box culvert.

As part of the District’s Stream Maintenance Program 2 (SMP2), after construction is complete, District
maintenance staff would periodically remove sediment as needed to ensure the capacity of the channel
is sufficient to convey the design flow, mow or spray vegetation to facilitate access and reduce fire
hazards, and inspect access roads for erosion or blockagesobstructions. Maintenance staff would also
inspect and repair structures such as rock revetment, concrete linings, and stormwater outfalls as
needed. The District would also remove trash or obstacles that may hinder flood flows. Because the
improved channel would more efficiently pass flood flows and would be less prone to erosion, future
maintenance needs would be reduced compared to current conditions.

SMP2 is an ongoing District activity that is not part of the proposed project. SMP2 activities are
permitted by regulatory agencies and all SMP2 activities on Upper Berryessa Creek will be implemented
in conformance with the SMP2 permits. The cumulative impacts section of this EIR addresses potential
environmental effects of SMP2 activities that could add to the environmental effects of the proposed
project.

After construction of the proposed project is completed, the District would continue the ongoing SMP2
maintenance practices at the Upper Berryessa Creek project area, and would add measures to
maintainperform inspection of the newly constructed floodwalls and culverts. Additional maintenance
activities associated with the project include inspection and graffiti abatement at floodwalls and
culverts, and additional access road inspections, and maintenance. These activities would occur
regularly to maintain channels and structures at design conditions.

ES.6 SUMMARY OF ALTERNATIVES
In accordance with CEQA Guidelines § 51526.6(a), this EIR analyzes four alternatives to the proposed
project. They are intended to provide a range of alternative actions that could feasibly achieve the
project objectives while avoiding or substantially reducing significant environmental impacts. The
alternatives are as follows:
• No Project Alternative
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• Alternative 2A: U.S. Army Corps of Engineers Selected Project
• Alternative 2B: Expanded Incised Trapezoidal Channel (FEMA Certification Performance)
• Alternative 4: Walled Trapezoidal Channel (FEMA Certification Performance)

The proposed project would achieve all project objectives (see Table ES-1).The No Project Alternative
would not meet project objectives and is analyzed in this EIR for comparison purposes. Alternatives 2A,
2B, and 4 would partially meet project objectives. Specifically, Alternative 2A would not meet FEMA
certification standards and would only partially achieve Objective 1. Alternatives 2B and 4 would meet
Objectives 1 and 2, but would not meet Objective 3 (Be consistent with USACE-selected plan).

Table ES.1: Project Alternatives Compared to Project Objectives
Alternative Objective 1 Objective 2 Objective 3
Proposed Project Meets Meets Meets
No Project Does not meet Does not met Does not meet
Alternative 2A Partially meets Meets Meets
Alternative 2B Meets Meets Does not meet
Alternative 4 Meets Meets Does not meet

These alternatives and the proposed project are analyzed in this EIR to determine the environmentally
superior alternative. Based on the evaluation of potential impacts presented in Chapters 3, 4, and 5 of
the Draft EIR, the proposed project is environmentally superior because it would accomplish the project
objectives (reduce flood damages, incorporate environmentally sustainable design practices, and be
consistent with the USACE’s selected plan) while minimizing construction-period environmental impacts.

ES.7 IMPACTS AND MITIGATION MEASURES
Table ES-2 identifies potential impacts that would occur under the various alternatives. With the
exception of impacts to air quality, construction noise, and emissions of greenhouse gases, all significant
environmental impacts could be reduced to less than significant levels by implementing mitigation
measures described at the end of each resource section.

For all alternatives other than the No Project Alternative, emissions of nitrogen oxides (NOx), temporary
noise impacts during construction, and greenhouse gas emissions would exceed applicable significance
thresholds. Feasible measures to mitigate these impacts are identified in this EIR, but would not reduce
these impacts to a less than significant level. These impacts would be significant and unavoidable under
the proposed project, as well as under Alternative 2A, Alternative 2B, or Alternative 4.

The cumulative impacts of the proposed project and alternatives combined with impacts from other
recent, ongoing, or reasonably foreseeable projects were also assessed. This analysis found that, in
combination with other projects, the proposed project would make cumulatively considerable
contributions to significant cumulative impacts on air quality, noise, and greenhouse gas emissions. In all
other resource categories, cumulative impacts would either be less than significant, or if the cumulative
impact would be significant, the proposed project’s post-mitigation contribution to the impact would
not be cumulatively considerable.

ES.8 AREAS OF KNOWN CONTROVERSY
The District issued a Notice of Preparation and invited individuals, organizations, and agencies to
comment on the scope of the Draft EIR in October, 2001. Notable concerns focused on addressing
degradation of natural resources by reducing channelization and eliminating concrete lining to the
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degree possible; designing the channel to allow for natural fluvial processes to occur; positioning
maintenance roads outside of the channel; and ensuring that the completed project accommodates
existing storm drainage facilities at any State highway bridge crossings.

USACE and the District have addressed these concerns in the project designs, as reflected in this Draft
EIR. Although the proposed project evaluated in this Draft EIR is reduced in scope from the project as
proposed in 2001, the design includes widened channel that will allow for more natural fluvial
processes, and which has an earthen bottom except beneath bridges and culverts; maintenance roads
positioned in the overbank areas except for ramps needed to allow access to the channel bottom; and
storm drainage facilities that are maintained or improved relative to their original condition. Other areas
of controversy have not been identified.

ES. 9 ISSUES TO BE RESOLVED
Consultation between the project sponsors and permitting agencies has either been initiated or will be
required in order to resolve any permitting issues that may arise. USACE regulations generally require
USACE to seek Section 401 water quality certification for USACE projects involving a discharge into
waters of the U.S. even though USACE does not issue itself a Section 404 permit. However, the project,
as a project authorized by Congress that has completed an EIS, qualifies for exemption under 33 U.S.
Code 1344(r). USACE will either obtain a Section 401 water quality certification or claim exemption
under 33 U.S. Code 1344(r) for the proposed project. Also, USACE will refine the project design to
determine the most appropriate location and sizes of mitigation areas for planting of native tree and
shrubs in accordance with the U.S. Fish and Wildlife Service Coordination Act Report of April 2013 and
follow-on consultations between USACE and USFWS.

Maintenance and operation of the reconstructed creek channel would be the responsibility of the
District. Most maintenance activities would be similar to the creek maintenance activities currently
performed under the District Stream Maintenance Program (SMP). Regulatory permits for the SMP
cover vegetation management, sediment removal, bank stabilization, management of animal conflicts,
and minor maintenance (e.g. fence repairs, access road maintenance, minor sediment removal of less
than 25 cubic yards, graffiti abatement), which would be the same activities needed to maintain the
creek after construction is complete. However, the reconstructed creek channel would be widened
compared to the existing channel and the SMP permits may not account for the area of channel
enlargement. If necessary maintenance activities are not covered by SMP permits, the District would
obtain approval and permits for the uncovered activities from The San Francisco Bay Regional Water
Quality Control Board, California Department of Fish and Wildlife, and USACE Regulatory Branch as
required by law.

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Table ES.2 Summary of Significant Effects, Mitigation Measures, and Level of Significance by Alternative
PROPOSED PROJECT NO PROJECT ALTERNATIVE 2A ALTERNATIVE 2B ALTERNATIVE 4
Widened Trapezoidal ALTERNATIVE USACE-Selected Alternative Expanded Incised Trapezoidal Walled Trapezoidal Channel
ENVIRONMENTAL RESOURCE Channel (FEMA Certification Channel (FEMA Certification (FEMA Certification
Performance) Performance), Accommodate Performance)
Upstream Bypass Channel
KEY: (+) Impacts greater than for Proposed Project, (=) Impacts equal to Proposed Project, (-) Impacts less than for Proposed Project,
(NI) No Impact, (LS) Less than Significant Impact, (LM) Less than Significant Impact with Mitigation, (S) Significant Impact, (SU) Significant and Unavoidable Impact
* Although impacts associated with these resource types were determined to be less than significant, a mitigation measure is proposed, or a measure proposed to address
another significant impact would further reduce this already LTS impact.
Aesthetics No significant impacts (-) No significant impacts No significant impacts No significant impacts No significant impacts
BIO-B: Compensate for Trees Removed
   
During Construction*
Significance Determination Before
LS NI LS LS LS
Mitigation/After Mitigation
NOx emissions above (-) No significant impacts (=) NOx emissions above (+) NOx emissions above (+) NOx emissions above
Air Quality BAAQMD thresholds (AIR- BAAQMD thresholds BAAQMD thresholds BAAQMD thresholds
2 and AIR-3) (AIR-2 and AIR-3) (AIR-2 and AIR-3) (AIR-2 and AIR-3)
AIR-A. Reduce Construction Period Dust
   
Emissions
AIR-B. Reduce Construction Equipment
   
Emissions
Significance Determination
S / SU NI S / SU S / SU S / SU
Before Mitigation / After Mitigation
Agriculture and Forestry None None None None None
Significance (No Mitigation) NI NI NI NI NI
Adverse impacts on (-) No significant impacts (=) Adverse impacts on (+) Adverse impacts on (+) Adverse impacts on
riparian habitat and riparian habitat and riparian habitat and riparian habitat and
healthy trees/shrubs (BIO- healthy trees/shrubs (BIO- healthy trees/shrubs (BIO- healthy trees/shrubs (BIO-
2).Adverse impacts on 2). 2). 2).
Biological Resources bird migration (Impact Adverse impacts on bird Adverse impacts on bird Adverse impacts on bird
BIO-4). migration (Impact BIO-4). migration (Impact BIO-4). migration (Impact BIO-4).
Conflict with policies in Conflict with policies in Conflict with policies in Conflict with policies in
Milpitas Tree Ordinance Milpitas Tree Ordinance Milpitas Tree Ordinance Milpitas Tree Ordinance
(BIO-5) (BIO-5) (BIO-5) (BIO-5)
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PROPOSED PROJECT NO PROJECT ALTERNATIVE 2A ALTERNATIVE 2B ALTERNATIVE 4
Widened Trapezoidal ALTERNATIVE USACE-Selected Alternative Expanded Incised Trapezoidal Walled Trapezoidal Channel
ENVIRONMENTAL RESOURCE Channel (FEMA Certification Channel (FEMA Certification (FEMA Certification
Performance) Performance), Accommodate Performance)
Upstream Bypass Channel
BIO-A. Perform Pre-Construction Nesting
   
Bird Surveys
BIO-B. Compensate for Trees and Shrubs
   
Removed During Construction
BIO-C. Use native grasses and forbs to
   
hydroseed disturbed areas.
BIO-D. Provide Buffers Around Riparian
   
Trees
Significance Determination
S / LM NI S / LM S / LM S / LM
Before Mitigation / After Mitigation
Adverse impact on (=) No significant impacts (=) Adverse impact on (+) Adverse impact on (+) Adverse impact on
historical/archaeological historical/archaeological historical/archaeological archeological site CA-SCL-
site CA-SCL-593 (Impact site CA-SCL-593 (Impact site CA-SCL-593 (Impact 593 (Impact CUL-1 and
CUL-1 and CUL-2) CUL-1 and CUL-2). CUL-1and CUL - CUL-2).
Cultural Resources Potential adverse impacts Potential adverse impacts 2).Potential adverse Potential adverse impacts
on unknown cultural on unknown cultural impacts on unknown on unknown cultural
resources and human resources and human cultural resources and resources and human
remains ( CUL-4) remains (CUL-2 and CUL- human remains (CUL-2 remains (CUL-2 and CUL-
4) and CUL-4) 4)
CUL-A. Implement the CA-SCL-593 MOA
    
and HPMP
CUL-B. Archaeological Monitoring and
   
Unanticipated Discovery Plan
Significance Determination
S / LM S / LM S / LM S / LM S / LM
Before Mitigation / After Mitigation
Potential to expose (-) No significant impacts (-) Potential to expose (+) Potential to expose (+) Potential to expose
structures or engineered structures or structures or structures or
slopes to adverse effects engineered slopes to engineered slopes to engineered slopes to
from seismic ground adverse effects from adverse effects from adverse effects from
Geology, Soils, and Mineral Resources shaking (GEO-1). Potential seismic ground seismic ground seismic ground
for soil erosion or loss of shaking (GEO-1). shaking (GEO-1). shaking (GEO-1).
topsoil (GEO-2) Potential for soil Potential for soil Potential for soil
erosion or loss of erosion or loss of erosion or loss of
topsoil (GEO-2) topsoil (GEO-2) topsoil (GEO-2)
GEO-A. Implement Geotechnical
   
Recommendations
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