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FINAL Supplemental
EIS/EIR
Acquisition of
Additional Water for Meeting the San Joaquin River
Agreement Flow Objectives, 2000 – 2010
Index
1. INTRODUCTION
The U.S. Bureau of Reclamation (Reclamation) and
the San Joaquin River Group Authority (SJRGA) are
jointly preparing this Supplemental Environmental
Impact Statement/Environmental Impact Report (SEIS/EIR)
to provide for the acquisition of up to 47,000 acre-feet
of "supplemental" water if needed by Reclamation
from the SJRGA and its members. The supplemental
water is to provide full Vernalis Adaptive Management
Plan (VAMP) test flow conditions at Vernalis during
"double-step years" for Water Years 2001
through 2010.
This document is a SEIS/EIR covering minor additions
to the project addressed in the Meeting Flow
Objectives for the San Joaquin River Agreement,
1999-2010, Final Environmental Impact Statement/Environmental
Impact Report (Final EIS/EIR, Reclamation 1999).
It documents the environmental consequences of acquiring
and using flows specified in the San Joaquin River
Agreement (SJRA). This chapter describes the purpose
of the Proposed Action or Project, why it is needed,
and what the Project proposes to accomplish, objectives.
It also provides information on the history of the
Proposed Project and the regulatory authority to
conduct the Project.
The SJRA developed as an alternative that provides
a level of protection equivalent to the San Joaquin
River flow objectives contained in the State Water
Resources Control Board’s 1995 Water Quality
Control Plan for the San Francisco Bay/Sacramento-San
Joaquin Delta Estuary (1995 WQCP: State Board
1995a). Discussion over the flow objectives led
to a proactive problem-solving process to develop
an adaptive fishery management plan. The water supplies
to support that plan were obtained from members
of the SJRGA. The SJRA is a "performance agreement"
(VAMP flows) and a water acquisition program (other
flows) wherein Reclamation and the California Department
of Water Resources pay the SJRGA to ensure that
water supplies are available for instream flows
as needed up to prescribed limits.
Reclamation proposes to contract for water on the
Tuolumne and Merced rivers under PL 102-575, Title
34, Section 3406(b)(3) of the Central Valley Project
Improvement Act (CVPIA).
1.1 HISTORY OF
PROJECT
On December 15, 1994, the federal government, the
State of California, and urban, agricultural and
environmental interests reached the principles for
agreement on a comprehensive, coordinated package
of actions designed to provide interim protection
to the San Francisco Bay and Sacramento-San Joaquin
River Delta Estuary. That agreement is referred
to as the 1994 Bay-Delta Accord, which was extended
to December 15, 1998. Many of the coordinated package
of actions agreed upon in the Accord were subsequently
adopted by the State Board in their 1995 WQCP (95-1
WR by State Board Resolution No. 95-24).
In June 1995, the San Joaquin Tributaries Association
filed a lawsuit over the State Board’s adoption
of the 1995 WQCP. The Association’s complaint
asserted that the 1995 WQCP was invalid for several
reasons, chief among those reasons was (1) the lack
of adequate scientific review and data necessary
to design a flow objective for the San Joaquin River;
(2) inadequate capability of the San Joaquin Basin
water users to supply these flows without significant
social and economic harm; and (3) the dispute over
the State Board's authority to require senior water
rights holders to supply increased flows while the
junior export projects were still allowed to pump
significant quantities of San Joaquin River flow.
In May 1996 the SJRGA proposed an alternative that
provides a level of protection equivalent to the
San Joaquin River flow objectives in the 1995 WQCP
in an effort to resolve the issues related to this
legal dispute. This proposed agreement was presented
to the state and federal governments in a document
titled "A Letter of Intent among Export Interests
and San Joaquin River Interests to Resolve San Joaquin
River Issues Related to Protection of Bay-Delta
Environmental Resources" and became known as
the Letter of Intent. The letter resulted in an
attempt to resolve the San Joaquin River flow objective
dispute through a consensus-building process.
A "Conceptual Framework
for Protection and Experimental Determination of
Juvenile Chinook Salmon Survival within the Lower
San Joaquin River" (SJRA Appendix
A) in response to river flow and State Water
Project/Central Valley Project (SWP/CVP) exports
was developed by Dr. Bruce Herbold and Dr. Chuck
Hanson. From that study framework, a collaborative
effort of scientists from state and federal agencies
and stakeholder groups developed the VAMP to gather
additional scientific fisheries information on the
lower San Joaquin River. Based on the San Joaquin
River flow and export targets identified in VAMP,
a program was developed among the state and federal
resource agencies, export interests, environmental
community representatives, and San Joaquin River
stakeholders. This process culminated in the development
of the SJRA. The VAMP study joined with the other
provisions of the SJRA provides environmental benefits
in the lower San Joaquin River and Delta, at a level
of protection equivalent to the 1995 WQCP for the
duration of the Project.
In 1997, prior to completion of the SJRA, Reclamation
initiated a 1-year water acquisition on the San
Joaquin River to help meet the VAMP Target Flows.
In 1998, water acquisition contracts were completed
with willing sellers to ensure that water would
be available for the 1998 Spring Pulse Flow.
In January 1999, the Final EIS/EIR was released;
the SJRA flow objectives were approved and confirmed
in the Water Right Decision 1641 (State Board 1999).
The SJRA contains three flow components:
- It obligates the SJRGA and its members to provide
the amount of water needed to achieve the April
- May Target Flow for VAMP or 110,000 acre-feet,
whatever is less. Additional water, in excess
of the 110,000 acre-feet required to be provided
by the SJRGA members, may be purchased from willing
sellers to meet the target flow for VAMP.
- The SJRA provides for Merced ID to sell 12,500
acre-feet above the existing flow for release
to the Merced River during October of all years
as an attraction flow for fall-run Chinook salmon.
- The SJRA also provides for OID to sell 15,000
acre-feet in every year of the SJRA plus the difference
between the water made available by OID for VAMP
pulse flow (11,000 acre-feet) and the amount actually
used. The additional water from OID could be used
for ramping either during the spring or October
pulse flows or at other times to supplement spawning
flows. The final decision for the use of this
water for fish and wildlife purposes would be
made annually by the Service, following consultation
with other federal and state agencies.
The Final EIS/EIR did not specifically address
the environmental impacts associated with acquiring
the additional "supplemental" water for
the Spring Pulse Flow above the 110,000 acre-feet
to be provided by SJRGA members. As noted in the
Final EIS/EIR (p. 2-5): "If achieving the double-step
requires more than the 110,000 acre-feet of supplemental
water, additional water from willing sellers on
the San Joaquin, Stanislaus, Tuolumne, and Merced
rivers (approximately 50,000 acre-feet) may be acquired
by Reclamation for the pulse flow period, and it
would require additional [National Environmental
Policy Act/California Environmental Quality Act]
NEPA/CEQA analysis". This SEIS/EIR provides
the required environment documentation to allow
the acquisition of the supplemental flows for the
period from 2001 through 2010.
1.2 PURPOSE OF AND NEED
FOR ACTION
As required under NEPA, this section presents a
concise statement of the Proposed Action’s
purpose and need, followed by a more complete explanation.
1.2.1 Statement
of Purpose and Need
Up to 47,000 acre-feet of water may be needed in
addition to the 110,000 acre-feet of water identified
in the SJRA for the VAMP 31-day Spring Pulse Flow
during April and May for Water Years 2001 through
2010. The purpose of the Proposed Project/Proposed
Action is to supplement, under Paragraph 8 of the
SJRA, the water provided by the SJRA, which has
been analyzed in the Final EIS/EIR (Reclamation
1999). This water is needed to support the flows
identified in VAMP by providing flows in the San
Joaquin River at Vernalis, and to assist Reclamation
in meeting the Anadromous Fish Restoration Program
(AFRP), Bay-Delta flow objectives as required by
Water Right Decision 1641 (State Board 1999), and
the Delta Smelt Biological Opinion (Service 1995a).
This water is needed to support the VAMP. The adaptive
management study is designed such that the flow
requirement can change annually in response to hydrologic
and biologic conditions. As a result, varying amounts
of water would be needed. Because the water would
increase instream flows in the lower San Joaquin
River, it would help to ensure compliance with the
1995 WQCP Vernalis objectives and with the 1995
Delta Smelt Biological Opinion.
1.2.2 Explanation
of Need for Project
The Bay-Delta Estuary is a critically important
part of California’s natural environment and
economy. In recognition of the serious environmental
problems facing the region and the complex resource
management decisions that must be made, the federal
government and the State of California are working
together with stakeholders to stabilize, protect,
and restore ecological health and improve water
management for beneficial uses in and from the Bay-Delta
Estuary. The Proposed Project is needed to provide
necessary information on what flows are needed in
the San Joaquin River system. The results of the
adaptive management studies will be evaluated to
help determine the appropriate Vernalis flow objective
after 2010.
The SJRGA is working cooperatively with the state
and federal agencies to assist in meeting the following
needs as explained below: increased instream flows,
the 1995 WQCP Vernalis objectives, and the Biological
Opinion on Delta Smelt (the 1995 Operations Criteria
and Plan opinion and the April 26, 1996, opinion
on temporary barriers).
1.2.2.1 Increased Instream Flows
Section 3406(b)(1) of the CVPIA requires the development
of a program that will "….make all reasonable
efforts to ensure that, by the year 2002, natural
production of anadromous fish in Central Valley
rivers and streams will be sustainable, on a long-term
basis, at levels not less than twice the average
levels attained during the period of 1967-1991.
. . ." As one element of the Draft AFRP, Reclamation
has a need to obtain this supplemental water on
the Tuolumne and Merced rivers to provide additional
flows at times that will facilitate emigration of
salmon smolts on these rivers in accordance with
specific fish, wildlife, and habitat restoration
purposes authorized by the CVPIA.
1.2.2.2 1995 Water Quality Control Plan Objectives
The State Board approved the final WQCP in May
1995. The 1995 WQCP includes objectives for Delta
outflow, Sacramento and San Joaquin River flows,
salinity, dissolved oxygen, and SWP and CVP operations.
It presents a combination of Delta inflow and outflow
objectives, water quality objectives, and Project
operation criteria. These requirements are specified
temporally and vary depending on the hydrologic
condition and the biological needs of various fish
species.
On December 29, 1999, the State Board issued its
Water Right Decision 1641 in the matter of implementation
of water quality objectives for the Bay-Delta Estuary,
a petition to change points of diversion of the
CVP and SWP in the southern Delta, and a petition
to change places of use and purposes of use of the
CVP. Section 10.2.1 notes the causes of salinity
concentrations at Vernalis. Salinity at Vernalis
is affected by the salt load and quantity of flow
in the lower San Joaquin river. High salt loads
and low flows at Vernalis result from a combination
of upstream water diversions, discharges of saline
drainwater, and subsurface accretions to the river
from groundwater. The State Board found that the
actions of the CVP are the principal cause of salinity
concentrations exceeding the objectives at Vernalis.
The capacity of the lower San Joaquin River to assimilate
the agricultural drainage has been significantly
reduced through the diversion of high quality flows
from the upper San Joaquin River. The order amends
the CVP permits under which Reclamation delivers
water to the San Joaquin River Basin to require
that Reclamation meet the 1995 Bay-Delta Plan
salinity objectives at Vernalis.
The flow objectives for the San Joaquin River as
measured at Vernalis have been debated in regard
to the inadequacy of scientific information relating
to salmon smolt survival. In an effort to clarify
the scientific basis for the flow objective and
resolve the uncertainty, the San Joaquin River and
state/federal export interests (federal and state
agencies, irrigation districts, water authorities,
and other water interests) collaborated to identify
feasible voluntary actions to protect the San Joaquin
River’s fish resources; help implement the
State Board’s fishery objectives; and evaluate
flow, head of Old River Barrier, export pumping,
and salmon smolt survival relationships. This collaboration
led to a scientifically based adaptive fishery management
plan now known as the VAMP. The SJRA to implement
VAMP provides the basis for the project information
given here and in Chapter 2. The SJRA provides water
to enhance instream flows for anadromous fish and
a methodology for establishing flows.
1.2.2.3 Delta Smelt Biological Opinion
The Delta Smelt Biological Opinion (Service 1995a),
approved Reclamation’s operations to provide
flows and pursue acquisition of additional water
(acquired flow) to provide San Joaquin River flows
at Vernalis in excess of those exported by the CVP
and SWP. Any such enhancement flows would be in
excess of those attributable to CVP New Melones
releases, unregulated accretions, or unstorable
flows, and would not be exported at the Delta pumping
facilities. As a result of this Opinion, Reclamation
has the authority to acquire water within the San
Joaquin River Watershed to maximize the ability
of the CVP to meet this commitment.
1.3 PROJECT OBJECTIVES
As required under the CEQA Guidelines [Section
15124(b)], this section identifies project objectives.
The Proposed Project’s objective is to acquire
water secured from willing sellers to provide Spring
Pulse Flow for the San Joaquin River system as identified
in the SJRA. The additional instream flows consist
of supplemental water for the 31-day pulse flow
during April and May under hydrologic conditions
that require a higher flow than can be accomplished
with the current 110,000 acre-feet. A description
of the proposed stream flow enhancements, or underlying
action with specific quantities by willing seller,
is provided in Section 2.1, Proposed Action.
Flows for VAMP would be targeted to reach the Vernalis
gaging station on the San Joaquin River. The specific
objectives of VAMP are: (1) to implement protective
measures for San Joaquin River fall-run Chinook
salmon within the framework of a carefully designed
management and study program that is designed to
achieve, in conjunction with other non-VAMP measures,
a doubling of natural salmon production by improving
smolt survival through the Delta; (2) to gather
scientific information on the effects of flows in
the lower San Joaquin River, CVP and SWP export
pumping rates, and operation of a fish control structure
at the head of Old River, on the survival and passage
of salmon smolts through the Delta; and (3) to provide
environmental benefits in the lower San Joaquin
River and Delta at a level of protection equivalent
to the San Joaquin River portion of the 1995 WQCP
for the duration of the SJRA (1999-2010).
The VAMP is also intended to provide benefits through
managed and unmanaged flow regimens (underlying
action), reduced rates of export during the Spring
Pulse Flow Period (related action), and installation
of a fish control structure at the head of Old River
(related action). All of these actions are expected
to contribute to improved conditions to help reach
the goal of doubling natural production of Chinook
salmon, consistent with the provisions of state
and federal law. Some of these actions (exports
and barrier operation) are not part of this document’s
Proposed Action, which is to provide only the supplemental
water to support VAMP in selected years over the
2001 – 2010 period.
1.4 AUTHORITY
FOR PROJECT
The authority for the Proposed Project/Action is
derived principally from the CVPIA. The CVPIA amended
the purposes of the CVP to achieve a reasonable
balance among competing demands for use of CVP water
for fish and wildlife, agriculture, municipal and
industrial, and power contractors.
Section 3406(b)(1) requires the development and
implementation of a program (AFRP) that will make
all reasonable efforts to ensure that, by the year
2002, natural production of anadromous fish in Central
Valley rivers and streams will be sustainable on
a long-term basis, at levels that are at least twice
the average levels attained during the period 1967-1991.
Reclamation will attempt to meet these requirements
through habitat and instream flow improvements in
the Delta and the San Joaquin River Basin.
Water may be acquired by Reclamation to meet fish
and wildlife needs within the San Joaquin Valley
under the authority of Section 3406(b)(3) of the
CVPIA. Section 3406(b)(3) provides for the acquisition
of water from willing sellers on the streams for
the following two specific purposes: ". . .
to supplement the quantity of water dedicated to
fish and wildlife purposes under Section 3406(b)(2)
. . . and to fulfill the Secretary’s obligations
under Section 3406(d)(2). . . ." Water obtained
from willing sellers would be used to provide increased
instream flows in specific months to improve habitat,
in accordance with preliminary information developed
by the AFRP. Acquiring water for the proposed action
on the Tuolumne and Merced rivers is authorized
specifically under this section of the CVPIA.
In addition, the CVPIA Final Administrative
Proposal on the Management of Section 3406(b)(2)
Water (Reclamation 1997a) identifies supplemental
instream flows, including a 31-day pulse flow during
April and May for VAMP.
1.5 RELATED PROJECTS
This SEIS/EIR adds to the program to manage resources
in the San Francisco Bay-Delta Estuary. Figure 1.5-1
of the Final EIS/EIR illustrates how that Final
EIS/EIR relates to other major projects and programs
in the Bay-Delta region. This SEIS/EIR, as a supplement
to the Final EIS/EIR, also covers a water management
program for the San Joaquin River system, and this
system is also affected by the other programs. The
SJRA water under CVPIA Section 3406 (b)(3) influences
the following actions:
State Board Bay-Delta Process (SWRCB 95-1)
including water rights hearings
CVPIA (especially Section 3406(b)(2))
Interim South Delta Program (Reclamation and
California Department of Water Resources)
CALFED Bay-Delta Program
Each of these actions is described in Chapter 14,
Cumulative Effects.
Final SEIS/EIR
Introduction |
March 13, 2001
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