Three Amigos

Three Amigos is also known as the Non-structural Alternative at the San Joaquin River National Wildlife Refuge

Updated on 2/4/2022: Potential Project Partner, Project Cost, and Project Status

Project Lead: San Joaquin River National Wildlife Refuge

Potential Project Partners:
iver Partners, United States Fish and Wildlife Service Anadromous Fish Restoration Program, United States Army Corp of Engineers, early project partners - USDA/Natural Resources Conservation Service, California Department of Water Resources, CALFED

Short Project Description:
Project to restore flooding and transient floodwater storage to more than 3,100 acres of historic floodplain, restore riparian habitats, and promote river physical processes of scour and deposition along 3 miles of the San Joaquin River. While the lands have been purchased, additional investment is needed to implement flood risk reduction goals consistent with the Refuge’s habitat management goals. Needed efforts include planning and design of the Refuge for flood management as well as removal of levees from the federal project.

Long Project Description:
As a result of the January 1997 floods, the San Joaquin River National Wildlife Refuge (SJRNWR) is working with the US Army Corps of Engineers (USACE) to plan a non-structural flood management alternative (NSA). This alternative includes breaching existing mainstem San Joaquin River levees on refuge land to protect and restore riverine and riparian habitat. This proposed NSA will provide floodplain inundation behind project levees of up to 3,100 acres on the Refuge in some years. The focus of the NSA study, being led by the USACE, has been to identify potential levee breech sites and evaluate potential flooding risk to adjacent landowners. The proposed scope of work will take the next step to identify and explore the potential impacts of the NSA alternative and help to refine this alternative to insure benefits to native aquatic, terrestrial, and avian species. Additional effort beyond the USACE study is needed to examine the potential impacts to existing infrastructure. It will also be necessary to assess potential hazards to wildlife caused by floodplain inundation, particularly terrestrial mammals. The adequacy of constructed floodwater refugia will need to be evaluated, particularly with respect to the endangered riparian brush rabbit.

This project will accomplish all the steps needed to allow implementation of the NSA to proceed. It will build on the technical studies and NSA alternative development that has occurred to date. These include the prior and current USACE NSA analysis, floodplain topographic data generated by DWR for the FloodSAFE Program, and the current study funded by DWR to develop a Water Control Structure design concept for the Refuge. Evaluation of potential resource management issues and monitoring of interim flood conditions prior to full NSA implementation will help the SJRNWR to identify and design the optimal combination of management and infrastructure modifications to meet flood risk reduction objectives while at the same time providing benefits to juvenile Chinook salmon, steelhead, and other native fish species, as well as native wildlife, including riparian obligate birds and mammals. These analyses and additional effort will be required to support the project through any necessary USACE and Central Valley Flood Protection Board procedural steps to allow implementation of the NSA, in addition to environmental documentation and permitting.

Unique Project Characteristics:
The envisioned use of the Refuge as connected floodplain and a site for transitory flood storage would be a remarkable ecological asset in the region and would benefit many endangered and native species in the San Joaquin River Basin. In particular, the proximity of the SJRNWR to salmon-producing tributaries is such that all juvenile salmonids produced in the Tuolumne and Merced rivers pass through riverine habitat of the SJRNWR. Improved floodplain habitat could provide additional beneficial rearing and growth opportunities in a mainstem system with very little remaining physical habitat diversity. Development and implementation of an NSA that considers fish benefits provides a unique opportunity to the SJRNWR to cooperate with other fish management interests in planning mainstem habitat improvements to benefit the native fish fauna.

Project Status In-progress
Project Cost $60,000,000
Project Timeframe More than 5 years
Cost-sharing No opportunities identified to date
Multi-benefit Project Yes
Types of benefits The project would improve flood risk management, promote ecosystem functions, and promote multi-benefit projects.
Source of Project USFWS AFRP

Background Information:
The USACE is the federal sponsor for all SPFC levees within the region. Under Public Law 84-99, the USACE is authorized, when requested by the non-federal sponsor of a flood work, to implement Non-Structural Alternatives (NSA’s) to the rehabilitation, repair, or restoration of flood works damaged by floods. Following the devastating floods in 1997, the USACE convened an Inter-Agency Task Force to evaluate the locations where levees failed in the San Joaquin Basin, and identify opportunities for NSA’s. Of 17 sites evaluated in the San Joaquin Basin, one rose to the forefront as an opportunity supported by many partners. The landowners in RDs 2099, 2100, and 2102 (collectively the “Three Amigos”) were willing to sell their flood-prone lands, and the USFWS was willing to accept ownership of those lands for management as flood-prone wildlife habitat and inclusion into the adjacent San Joaquin River National Wildlife Refuge (SJRNWR). The USDA NRCS partnered with USACE and USFWS to purchase perpetual floodplain easements on the lands; the USACE purchased flowage easements and the USFWS purchased the underlying fee title of the properties. Additionally, a Memoranda of Agreement was drafted and signed by the USFWS, USACE, and California Reclamation Board (now Central Valley Flood Protection Board) to implement the NSA.

Conceptually, the NSA included the purchase of flowage easements over the lands that were previously provided flood protection by the levees within the Three Amigos in lieu of the levee breach locations being repaired. This required modification to the maintenance manuals for these Reclamation Districts to eliminate the need to perform levee maintenance (i.e. the levees would be maintained in a breached condition as the levees no longer provide flood protection to the district lands). The USACE offered to construct ring levees around existing structures that would be exposed to more frequent flooding under the implementation of the NSA, however ring levees were not constructed at the request of the landowner. Flowage easements were offered on lands outside of the Three Amigos to ensure that unintended flood damages were compensated; however two landowners rejected the offer. Until these remaining landowners accept the flowage easements, the maintenance manual cannot be modified. Today, implementation of the NSA is still largely supported by the resource agencies and the original signatories to the MOA, however the required flowage easements have not yet been offered or accepted.

The Three Amigos cover an area of approximately 3,200 acres. During the 1997 flood event, four failures occurred on the west or left bank levee along the San Joaquin River flooded RDs 2099, 2100, 2101, and 2102. These levees were subsequently repaired even as steps were being taken to implement the Non Structural Alternative. Since that time, however, the SJRNWR has continued to experience flooding, most recently in late December 2010, early January 2011, and late March 2011. This flooding occurs as high river flows back up the West Stanislaus Irrigation District intake canal, which cuts across the SJRNWR between RD 2100 (Hagemann Tract) and RD 2102 (Lara Tract). The canal was at one time protected at its mouth by a levee penetrated by a dual box culvert connection to the canal which was damaged and removed some years ago. The canal is bordered by berms that are prone to overtopping and breaching in high water. At the end of December 2010, flood water flowed through such a breach and flooded a portion of the Lara tract. Flooding in late March 2011 resulted in extensive flooding at the SJRNWR, including both the Lara tract and the Hagemann tract. Drainage of floodwaters from behind breached levees often requires active pumping. Following flooding in the spring of 2006, pumps were inaccessible and lands on the dry side of the RD 2100 levee (Hagemann tract) were inundated for months after the river levels had receded. Such long duration flooding has negative impacts to natural areas, as was documented by River Partners (2008).

Hydraulic modelling to support the restoration of lands formerly protected by the Three Amigos levees has shown that high-elevation refugia and appropriately located levee breaches are needed to ensure that the wildlife habitat requirements of resident populations are met. Since 1997, the levee slopes across the majority of the Three Amigos have been vegetated with brushy native plants to provide cover for terrestrial species fleeing floodwaters, and over 30 acres of elevated refugia have been constructed in consultation with wildlife experts, flood management engineers, and resource agency personnel.

In 2010, DWR has invested in the Ecosystem Restoration and Floodwater Attenuation (ERFA) project at the SJRNWR which includes 551 acres of habitat restoration within the Three Amigos footprint as well as the construction of enhanced reconnection facilities to increase the frequency of inundation of the floodplain fields and to decrease the residence time for impeded floodwaters on the dry side of the levees. The final implementation of this construction will require realization of the NSA in the form of a revised maintenance manual for the SPFC facilities within the Three Amigos. The agencies continue to work to implement this important demonstration project and to illustrate the pathway for removal of levee maintenance obligations from federal project levees. Should other RDs in the Central Valley wish to implement similar NSAs, lessons learned through the implementation of the Three Amigos project may provide a cost savings and a time savings, although the ultimate implementation of the NSA project has yet to be seen.

In 2012, the 1600-acre Dos Rios Ranch was purchased by River Partners for management as flood-prone wildlife habitat and potentially as a transient floodwater storage basin. Funding for the acquisition was provided by the USDA NRCS, California Wildlife Conservation Board, DWR, the California River Parkways Program, the San Francisco Public Utilities Commission, the USFWS North American Wetland Conservation Act (NAWCA), the US Bureau of Reclamation and USFWS Central Valley Project Conservation Program, and River Partners. The USDA NRCS holds a Wetland Reserve Program easement, the Tuolumne River Trust holds a Conservation Easement, and River Partners holds the fee title for the property. In 2013, the remaining 497 acres of flood-prone land within Reclamation District 2092 (Dos Rios) were purchased by River Partners for similar purposes. The Tuolumne River Trust holds a Conservation Easement on the property which expressly provides for the future development of habitat mitigation opportunities for SPFC impacts on 191 acres of the property, and River Partners owns the fee title. River Partners hopes to use the NSA example from the Three Amigos project as a model for floodplain reconnection on the RD 2092 properties. Habitat restoration is currently underway and is expected to be completed in phases over the next 8 to 10 years. Restoration activities include screening river pumps to protect juvenile salmonids, earthwork to create floodplain swales and benches as well as high-elevation refugia for terrestrial species, planting, and ongoing vegetation maintenance, and eventual modification to the existing levee to provide for floodplain reconnection and transient floodwater storage. Additional funding and permitting is required to complete the full build-out of the Dos Rios Ranch Habitat Restoration Project.

The following are additional references on this project:

  • Portion of AFRP website that features the project here.
  • USFWS, 2006. San Joaquin River National Wildlife Refuge Final Comprehensive Conservation Plan. September 29. (Available here)
  • USACE, 2000. Memorandum of Agreement Between the Department of the Army and the United States Fish and Wildlife Service for Implementation of Nonstructural Alternative to the Repair or Restoration of Levees for Reclamation Districts 2099, 2100, and 2102. June 27.
  • USACE, 1998. PL 84-99 Nonstructural Alternative to Structural Rehabilitation of Levees, San Joaquin River Sub-basins 12 and 13, Reclamation Districts 2099, 2100, and 2102, Sacramento District. September.
  • USACE, 1997. FONSI (with: Environmental Assessment: PL 84-99 Levee Rehabilitation, Reclamation District 2099, San Joaquin River Basin, Stanislaus County, CA. July 29).