Resolving complex issues with large scale river restoration; a case study: the San Joaquin River in California

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1 IWA Publishing 2011 Water Practice & Technology Vol 6 No 4 doi: /wpt Resolving complex issues with large scale river restoration; a case study: the San Joaquin River in California William R. Swanson, P. E.* and Jill C. Chomycia** * Vice President, MWH Americas, 2121 N. California Blvd, Suite 600, Walnut Creek, California, 94596, USA. ** Senior Geologist, MWH Americas, 3321 Power Inn Road, Suite 300, Sacramento, California, 95826, USA. Abstract One of the largest river restoration efforts in the United States is now under way in the Central Valley of California. The San Joaquin River Restoration Program (SJRRP) was triggered by a 2006 Settlement, following over 18 years of litigation, between numerous environmental interest groups, water users, and the Federal government. Since the 1940s, Friant Dam on the San Joaquin River has provided water to approximately 1 million acres of agricultural lands, but also let to the extirpation of salmon runs. The Settlement has two primary goals: establish naturally producing and self-sustaining salmon in a 150-mile reach of the river, and reduce or avoid adverse water supply effects to the water users. The Settlement specifies flow requirements, and numerous actions to provide adequate channel capacity, establish fish habitat, introduce salmon, recover water supplies, and address adverse effects to third parties. Limited flows were initiated in October 2009 to support experimentation and data collection, while the implementing agencies continue to address long-term issues regarding environmental effects, flood protection, water recovery, development of channel capacity and fish habitat, and reintroduction of salmon. This paper describes some of the major issues that are being addressed to implement the restoration program, including program structure, project planning and permitting, protection of private lands, coordination of restoration actions with ongoing water delivery and flood management systems, financing challenges, and public participation and education. Key words: Equitable distribution of water, integrated river basin management, sustainable ecosystem, sustainable water supply, climate change effects, adaptive management BACKGROUND In 1988, a coalition of environmental groups, led by the Natural Resources Defence Council (NRDC) filed a lawsuit challenging the renewal of the long-term water service contracts between the United States and the Central Valley Project (CVP) Friant Division contractors. The CVP is the largest irrigation project operated by the U.S. Bureau of Reclamation (Reclamation), providing water to over 3 million acres of farmland and over 2 million people in the Central Valley and the San Francisco Bay Area. Initial longterm (40-year) contracts for Friant Division water deliveries were established in 1948, and were subject to renewal in The lawsuit contended that renewal of the long-term water contracts violated several environmental protection laws of the United States and the State of California. The friant division of the central valley project The Friant Division of the CVP includes facilities that deliver water to 28 water districts that in turn provide water to over 15,000 small family farms located in the eastern portion of the San Joaquin Valley. It encompasses approximately 1 million acres of some of the most productive farmland in the U.S. The Friant Division was part of the initial features of the CVP, constructed during the 1930s and 1940s. The main features of the Friant Division include Friant Dam on the San Joaquin River, and nearly 200 miles of canals.

2 Water Practice & Technology Vol 6 No 4 doi: /wpt Friant Dam on the San Joaquin River (SJR) was designed and operated to divert most of the water in the river and convey it through two canals to water users in the Friant Division. As a result of the operation of Friant Dam, portions of the SJR downstream of the dam became dry during extensive periods of most years, thereby extirpating historic salmon runs and other fisheries. The diversion of San Joaquin River flows at Friant Dam precludes delivery of water to senior water rights holders downstream. In exchange for the reduction in river flows, Reclamation signed a contract with these senior water rights holders, or Exchange Contractors, to deliver CVP water in exchange for river flow. To accomplish this exchange delivery, initial features of the CVP also included a pumping plant and canal to convey water from the Sacramento and San Joaquin Rivers Delta (Delta) to a pre-existing diversion facility on the San Joaquin River known as Mendota Pool, where water supplies are diverted by the Exchange Contractors. Under the exchange contract, Reclamation can deliver water to Mendota Pool to fulfill contract obligations through the canal or through the SJR at its discretion, subject to the terms of the contract. The settlement After more than 18 years of litigation of the lawsuit, a Stipulation of Settlement (Settlement) was reached in September 2006 by the Settling Parties and subsequently approved by the Court. The Settlement is founded on two parallel goals: The Restoration Goal: To restore and maintain fish populations in good condition in the main stem of the San Joaquin River below Friant Dam to the confluence of the Merced River (approximately 150 miles downstream), including naturally reproducing and self-sustaining populations of salmon and other fish. Central Valley salmon are anadromous and migrate through the San Francisco Bay-Delta to the Pacific Ocean. The Water Management agement Goal: To reduce or avoid adverse water supply impacts to all of the Friant Division long-term contractors that may result from the release of Interim and Restoration flows provided for in the Settlement. SETTLEMENT IMPLEMENTATION The Settlement and authorizing Federal legislation require that the Secretary of the Interior will implement the terms and conditions of the Settlement. Additionally, the Settling Parties agreed that implementation will require the involvement of the State of California. Implementation is being guided through the San Joaquin River Restoration Program (SJRRP), led by Reclamation in coordination with other Implementing Agencies, including the US Fish and Wildlife Service (USFWS), the US National Marine Fisheries Service (NMFS), the California Department of Fish and Game (DFG), and the California Department of Water Resources (DWR). The Settlement also established a Restoration Administrator (RA), supported by a Technical Advisory Committee and the Settling Parties, to work collaboratively with Reclamation in implementation. The RA recommends flow schedules and salmon reintroduction criteria, and provides input on project design, monitoring, and other relevant science-based activities. San Joaquin River restoration area Implementation of the Settlement has the potential to affect a large portion of California, as a result of operational changes that modify water delivery patterns, construction of channel improvements, restoration of continuous flow to the San Joaquin River, and modifications to the operation of water delivery systems. The geographic extent of the SJRRP implementation area includes the Central Valley from the Delta to the Tehachapi Mountains south of Bakersfield. This area includes the SJR

3 Water Practice & Technology Vol 6 No 4 doi: /wpt from Friant Dam to the Delta, the Friant Division of the CVP, other water service areas potentially affected by changes in water deliveries or restoration of the SJR, and tributaries to the SJR downstream from the river restoration area. The Restoration Area extends 153 miles downstream from Friant Dam to the confluence of the Merced River, the first downstream major tributary to the SJR. In recognition of different habitat, water quality and land management conditions along the SJR, the Restoration Area is divided into five primary reaches shown on Figure 1. Figure 1 San Joaquin River restoration area

4 Water Practice & Technology Vol 6 No 4 doi: /wpt Channel and structural improvements to support the restoration goal The Settlement acknowledges that achieving the Restoration Goal will require a combination of channel and structural improvements in the Restoration Area and releases of additional water from Friant Dam to support restoration priorities. The Settlement specifies a set of near-term and longer-term channel and structural improvements that will be necessary to safely convey Restoration Flows through locations known to have insufficient flow capacity, and a set of longer term improvements to enhance the effectiveness of restoration. Near-team improvements to provide additional flow capacity include extensive channel modifications to increase capacity in two river reaches (2B and 4B1) and construction of a new bypass to convey at least 4,500 cubic feet per second (cfs) with integrated floodplain habitat. These modifications will require construction of new levees and floodplain grading for about 40 river miles, and modifications to existing flow control structures that can allow the existing water delivery and flood control purposes to be met while supporting restoration objectives. Near-term improvements to address fish passage include screening a large water diversion (800 cfs), modifying diversion dams to enable fish passage, installing barriers on sloughs to prevent fish from straying, and modifications to flood conveyance facilities to improve channel stability and fish passage. Longer-term improvements include gravel augmentation in spawning areas, isolation of adjacent gravel pits to reduce predation of salmon by introduced species, establishment of side channel habitat, and other similar actions that would enhance restoration success. A generalized summary of channel and structural improvements to support restoration are shown on Figure 2. Restoration flow management The Restoration Goal of the Settlement includes six flow patterns based on hydrologic year types that specify total monthly volumetric releases from Friant Dam based on total annual inflow to Millerton Lake (formed by Friant Dam), and flow targets at several locations along the San Joaquin River. Hydrologic year-type Restoration Flow release patterns from Friant Dam are shown in Figure 3. Implementation of the Settlement required that a method be developed to convert these block allocations to a more continuous hydrograph that reflects both hydrologic variability and fishery life cycle requirements. A risk based approach is used, starting as early as January, to regularly revise inflow estimates in response to rainfall and snowpack conditions. As each updated forecast of total annual flow is completed, the revised annual release quantity is applied to a continuous allocation pattern, which is illustrated in Figure 4. Because the largest portion of the release pattern (April, May, and June) can occur before the total annual inflow is known (often not finalized until June), a risk-based method was developed to quantify the total annual flow requirement in relation to expected Millerton Lake inflow. The Settlement requires that flows be released from Friant Dam beginning October 1, 2009, even though the channel and structural modifications to convey full Restoration Flows would not be completed until later. An experimental interim flow program was included in the Settlement to provide for flow releases during the time that channel improvements would be performed, so long as the flows do not exceed then-existing capacity at any location in the Restoration Area. Interim Flows were initiated on schedule and continue, as illustrated in Figure 5. Data are being collected to improve the understanding of several physical and biological factors, including seepage, river water temperature and quality, surface watergroundwater interaction, riparian habitat responses, sediment transport, fish rearing and migration, downstream recapture of Interim and Restoration flows, and other data relevant to

5 Water Practice & Technology Vol 6 No 4 doi: /wpt restoration and water management goals. Data also are being collected by the State of California, as part of a related but separate program focused on flood protection, to improve the understanding of geotechnical conditions of levees and the river channel throughout the Restoration Area. These data are being used help estimate then-current capacity. Figure 2 San Joaquin River restoration program channel improvement and fish habitat actions

6 Water Practice & Technology Vol 6 No 4 doi: /wpt Figure 3 Restoration flow release schedules specified in the settlement Figure 4 Continuous annual restoration flow allocation strategy

7 Water Practice & Technology Vol 6 No 4 doi: /wpt Before Restoration July During Interim Flows November 2009 Figure 5 San Joaquin River Reach 2 before restoration and during initial interim flows Salmon reintroduction plan The Settlement requires the reintroduction of spring run and fall run Chinook salmon to the SJR between Friant Dam and the Merced River confluence no later than December 31, The USFWS is working diligently to prepare a permit application for the introduction of spring run Chinook salmon for review and approval by NMFS. A key consideration in the permit will be the source stock of spring run Chinook salmon from other Central Valley rivers. The Implementing Agencies also are considering the need for a hatchery to supplement initial fish populations. Recently, the effects of releasing Interim Flows and subsequent flood flows have attracted fall run Chinook salmon and other fish into the Restoration Area. As part of the Experimental Interim Flow program, juvenile fish are being released into the SJR immediately downstream of Friant Dam. These fish are being monitored to help identify priority issues to be addressed through water management and channel modifications to help achieve the Restoration Goal. Provisions to support the water management goal The Settlement requires that a plan for recapture, recirculation, reuse, exchange, or transfer of Interim and Restoration Flows be developed to reduce or avoid water supply impacts to all Friant Division long-term contractors. It also requires that a Recovered Water Account be established to track water supply reductions to all Friant Division contractors that result from the release of Interim or Restoration Flows. Through a Water Management work group, Reclamation continues to develop methods to recapture Interim and Restoration flows at downstream locations without adversely affecting the Restoration Goal, and convey the recaptured water to the Friant Division to help offset water supply reductions. The work group is considering water volume potentially available for recapture at critical locations along the SJR downstream of the Restoration Area and in the Delta, the timing of the available water supply, and issues related to conveying the recaptured water through CVP and California State Water Project (SWP) facilities without interfering with ongoing operations and water delivery obligations to others. Reclamation has obtained short-term permits and will obtain a long-term water right to protect Interim and Restoration flows from diversion by others to assure that these flows would be available for recapture at downstream locations.

8 Water Practice & Technology Vol 6 No 4 doi: /wpt The Settlement also provides that Friant Division water contractors may purchase unstorable water at Friant Dam (during flood operations) at a pre-established rate, up to the amount of reduced deliveries recorded in the Recovered Water Account. Because the water management goal provisions involve integration of new criteria with existing project operations, they require complex methods and accounting procedures to accurately reflect conditions that would have occurred in the absence of the SJRRP. Methods to estimate and account for water supply impacts, delivery of flood water, and recapture and delivery of Interim and Restoration flows have been developed and integrated into established water allocation and operation procedures for Friant Dam and other related CVP and SWP facilities. These methods will continue to be refined as implementation of the SJRRP progresses. CHALLENGES TO SUCCESSFUL IMPLEMENTATION Restoration of the San Joaquin River requires coordination, planning, and execution of many complex and inter-dependent activities on a large scale. Because the SJR had been so severely impaired prior to the Settlement, many issues regarding the condition of levees and channels, ecological responses, and surface water-groundwater interactions remain poorly understood. Accordingly, the SJRRP is being implemented in a manner that makes best use of available scientific information while allowing for flexibility to adapt actions in response to observations and new information. The following sections present the SJRRP approach to address some of the challenges facing implementation. Authorization, schedule and funding The Settlement included an aggressive schedule for implementation of channel improvements, release of full Restoration Flows and reintroduction of salmon. It also recognized the need for Federal legislation to authorize the Secretary of the Interior (through Reclamation) to implement the SJRRP. Although authorizing legislation was enacted in March 2009, over two years later than anticipated in the Settlement, Reclamation initiated Interim Flows in October 2009, consistent with the Settlement schedule. Table 1 shows milestone dates recommended in the Settlement. The Implementing Agencies are committed to attaining these milestones, as demonstrated by the release of Interim Flows beginning in October 2009; however, these dates may change, pending completion of compliance, coordination, consultation, data collection, and related efforts. Funding for Settlement actions derive from multiple sources and become available at various points time. The Federal legislation authorizing the Settlement established the San Joaquin River Restoration Fund and directed that revenue be deposited into the Fund from the following sources: Future receipts collected pursuant to a surcharge on water deliveries that was required of all Friant Division contractors under a separate law enacted in 1992 Authorized Federal appropriations Capital repayment from the Friant Division water contractors for remaining obligations related to the construction of CVP facilities Water sales of those portions of the Restoration Flows, if any, which cannot be released beginning January 2014 as a result of insufficient channel capacity. In addition, the State of California will expend bond funds authorized by the voters in 2008 to improve water management in and flood protection in California. The bond measures identify funding amounts for contribution toward SJR restoration. In total, funding provided through these sources is expected to be sufficient to implement improvements estimated at about $800 million.

9 Water Practice & Technology Vol 6 No 4 doi: /wpt Table 1 Key settlement milestones Date October 2009 September 2010 April 2012 December 2012 December 2013 January 2014 December 2016 December 2024 December 2025 January July 2026 Initiate Interim Flows and monitoring program Milestone USFWS submits a completed permit application to NMFS for reintroduction of spring-run Chinook salmon NMFS issues a decision on the permit application for reintroduction of spring-run Chinook salmon Reintroduce spring-run and fall-run Chinook salmon, if permitted by NMFS Complete Phase 1 improvements identified in the Settlement Secretary of the Interior, in consultation with NRDC and FWA, develops operational guidelines Initiate full Restoration Flows Complete Phase 2 improvements identified in the Settlement Secretary of Commerce reports to Congress on the progress made in reintroducing spring-run and fall-run Chinook salmon and discusses plans for future implementation of the Settlement Review and revise Restoration Flows, if necessary Any party to the Settlement may file a motion to request an increase, decrease, or material change in the quantity and/or timing of Restoration Flows Environmental permitting strategy Upon acceptance of the Settlement by the Court in October 2006, work began immediately on preparation of environmental compliance documentation consistent with the National Environmental Policies Act (NEPA) and the California Environmental Quality Act (CEQA). These laws require extensive public disclosure of the effects of proposed actions that would affect resources, and development of appropriate mitigation measures where possible. The environmental permitting strategy was designed to address short-term and long-term actions, and accommodate needed adaptation in Settlement implementation. The following types of environmental compliance documents are being prepared: A program environmental impact statement is being prepared to identify the collective effects of implementing all Settlement actions at a system-wide level, including flow modifications, construction actions, and fish reintroduction. This document also will provide compliance for the release and management of Interim and Restoration flows, and the application of a water right permit amendment to protect these flows for downstream recapture. Site-specific environmental assessments have been and will be prepared for the installation of facilities to monitor physical parameters, such as river flow, sediment movement, groundwater levels, and other related facilities. Short-term environmental assessments have been prepared to address effects related to the release of Interim Flows on an annual basis while the program environmental impact statement is being prepared. Site-specific environmental impact statements and environmental assessments are being prepared for each construction activity identified in the Settlement. Because the collective system-wide effects of all construction actions are addressed in the program environmental impact statement, the site-specific evaluations will be limited to assessments of impacts at each project location. Avoidance of third party impacts If not properly anticipated, implementation of Settlement actions has the potential to cause impacts to parties that were not part of the Settlement. The Restoration Area portion of the SJR, which is the focus of improvements to increase capacity, protect fish, and provide spawning and rearing habitat, flows

10 Water Practice & Technology Vol 6 No 4 doi: /wpt through private lands owned by parties not involved in the Settlement. Because the levees in the Restoration Area are not well designed, conveyance of Interim and Restoration flows through main-stem SJR reaches has the potential to cause seepage to adjacent lands. The SJRRP includes an extensive monitoring and management program to identify the potential for adverse impacts, and implement actions to avoid their occurrence or mitigate their effects. For example, in cases where the potential for seepage to increase exists, or if seepage is observed, flows would be reduced and/or compensatory measures would be taken. Access to private lands for monitoring, surveying or other observations is enabled through pre-negotiated temporary access permits and closely coordinated with landowners, irrigation districts, and levee management groups to avoid interference with ongoing agricultural activities, levee maintenance, or flood protection actions. Downstream of the Restoration Area, all tributaries that flow into the SJR are subject to flow requirements designed to protect fish and improve water quality. The introduction of Interim and Restoration flows from the Restoration Area into the lower portion of the SJR has the potential to alter baseline conditions and thereby affect flow requirements and reservoir operations on these tributaries. Through coordination with downstream tributary project operators, the Implementing Agencies are accounting for Interim and Restoration flows in a manner to avoid shifting additional water management obligations to these third parties. Also, strategies for the recapture and recirculation of Interim and Restoration flows involve the use of CVP and SWP facilities to convey and potentially store recaptured water supplies. Reclamation is working closely with project operators to assure that the recapture and conveyance of these water supplies does not adversely affect project operations or the availability of water supplies to CVP and SWP contractors. Integration with flood management operations The SJR in the Restoration Area serves as an integral portion of a regional flood control project, which includes a flood bypass system. Many levees along main-stem SJR reaches in the Restoration Area were not constructued in accordance with current Federal or State of California standards, and are prone to seepage, boils, erosion, and slope stability problems. The introduction of Interim and Restoration flows on a year-round basis complicates the operation and maintenance of these facilities, and has the potential to increase flood risk to protected lands. To avoid increasing flood risk, the SJRRP includes as set of performance standards that will be applied to estimate then-existing channel capacity based on levee integrity conditions. These estimates will be used to constrain maximum Interim and Restoration flows in the Restoration Area to avoid increasing flood risk. In addition, maintenance practices of the flood control project, including the bypasses, will be enhanced to provide vegetation and sediment management with the objective of preserving design channel capacity. Lastly, Interim and Restoration flows would be reduced in cases where their release and conveyance would interfere with flood operations. CONCLUSION Undertaking river restoration at the scale of the SJR requires adaptive strategies to address technical, legal, policy, management, and financial challenges. The Settling Parties anticipated many of these challenges and included provisions in the Settlement to enable continued progress toward achieving the Restoration and Water Management goals. SJRRP Implementation actions to date have begun to place these provisions into practice, which revealed additional challenges, as discussed in this paper. The Implementing Agencies are committed to successful restoration of the SJR and will continue to develop innovative and flexible responses to challenges as they arise.

11 Singapore International Water Week July 7, 2011 William R. Swanson, P.E. Water Resources Practice Leader The Setting

12

13 Sierra Nevada Mountains California Delta Central Valley Sierra Nevada Mountains California Delta Central Valley

14 San Francisco Friant Dam Friant Division Completed in 1942 Stopped river flow 1 million acres High value crops Small family farms Los Angeles San Diego San Francisco Friant Dam Friant Division 1 million acres High value crops Small family farms Completed in 1942 Stopped river flow Los Angeles San Diego

15 Shasta Dam San Francisco Friant Dam Completed in 1942 Stopped river flow Delta-Mendota Canal Replaces water to San Joaquin River Los Angeles San Diego Shasta Dam San Francisco Friant Dam Completed in 1942 Stopped river flow Delta-Mendota Canal Replaces water to San Joaquin River Los Angeles San Diego

16 Dry except during floods, about every 3 years Low conveyance capacity Dry Reach Drainage water only Flood flows only Low channel capacity Delta water enters river Diverted downstream Numerous gravel quarry pits connected to river

17 1948 Initial water contracts signed 1988 Contract renewal was challenged in Federal court Plaintiffs were 14 Environmental interest groups Defendants were Federal government and 22 irrigation districts 2006 Settlement reached after 18 years of litigation Environmental Coalition 14 organizations led by NRDC Settling Parties Friant Water Authority 22 water agencies Federal Government Bureau of Reclamation LEAD AGENCY Fish and Wildlife Service National Marine Fisheries Service State of California Department of Water Resources Department of Fish and Game Restoration Administrator Implementing Agencies 14

18 Restoration Goal To restore and maintain fish populations in good condition, including naturally reproducing and self-sustaining populations of salmon and other fish Water Management Goal To reduce or avoid adverse water supply impacts to all of the Friant Division longterm contractors that may result from the Interim Flows and Restoration Flows

19 Varies according to available supply Year-round base flow plus peaks Peak spring flows mimic snow-melt patterns Flow targets exist throughout river Forecasts include uncertainty bands Water banks for storage Flow schedules adjusted for needs of fish Sediment mobilization and cleaning Riparian vegetation Temperature management

20 Preserve design water level in all river reaches Provide for fish migration upstream and downstream Complex operations to avoid interference with The Restoration Goal Senior water rights Operations of major water projects Complex accounting Cannot exceed amount lost to Restoration Flow Rigorous monitoring of flows and losses Recovered water delivery and exchange Quantify Capture Convey Deliver Exchange

21 Change from intermittent flood flows Steady flows cause levee seepage Sediment and vegetation management Maintenance costs increase New information needed Characterize levee conditions Limit flows to safe capacity at all times Involve stakeholders in flow decisions Resolving Unexpected Issues Will Require More Time

22 Settlement and legislation provided funding for expected costs at the time Federal budget rules limit expenditures until 2018 Additional needs are being identified through detailed studies Current estimates approaching $1.5B Over-communicate with stakeholders and public officials Establish performance targets to guide actions Science-based processes assure agreement on the facts Comprehensive monitoring Adapt plans to changing conditions while meeting objectives

23 William R. Swanson, P.E. Water Resources Practice Leader Singapore International Water Week July 7, 2011

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