Establishing Roots: River Partners’ Long-term Efforts on the San Joaquin River NWR

By Tom Griggs, Ph.D.

Least Bell’s vireo nest in a San Joaquin River National Wildlife Refuge restoration site (2006)

In August 1999 River Partners sent me south to the San Joaquin River National Wildlife Refuge west of Modesto in the northern San Joaquin Valley. The Refuge had recently acquired about 3,100 acres on the west side of the river, immediately south of the Hwy 132 bridge. These acres had been farmland and a dairy before the floods of 1997. The three ownerships were severely impacted by the floods of January 1997, as they lie in a natural topographic bowl that rapidly filled with floodwater wherever the levees breached: they broke in 10 places along this reach causing Ed Hagemann’s house to go under water three times! The Natural Resource Conservation Service (NRCS) came forward to purchase a conservation easement over the properties and the Fish & Wildlife Service purchased fee-title. In addition, as a result of the flood damage, the Refuge units were designated a Non-Structural Flood Protection Demonstration Project by the Army Corps Of Engineers (ACOE), meaning that the ACOE levees that protected the properties from flooding would be breached in a strategic, engineered manner as part of the regional flood management program.

My job was to evaluate the restoration potential of the new West Units on The San Joaquin River NWR. The new Refuge lands had been under intensive, irrigated agriculture since the 1960s and some of it (the Vierra parcels) had been in cultivation prior to the 1920s. Intensive weed control over the years had taken its toll of native plants: two examples, the two largest valley oaks remained on either side of Hospital creek as it left the leveed portion of its channel. It was only at the base of these oaks that I could find a remnant patch of basket sedge and a small patch of creeping rye grass. (Creeping rye turned up in large patches in the southwest corner of the Lara property in an area of high water table that was not farmed.) The other example is that in 1999 there were no plants, native or weeds, growing on the sides of the main drainage ditch at field H20 – I remember being impressed by one lone mugwort plant hanging on the side of the canal! Today it is covered by thick weeds.

By contrast, I discovered the relict riparian meadow site. The relict meadow is about one acre in size and was apparently “left behind” when the Lara property was developed for agriculture. (It is against the levee and adjacent to a deep pond that may have been excavated or was eroded by an historical levee break.) The relict meadow is completely covered by several native herbaceous species. Individuals of weedy species are rare. This is the only not-plowed Columbia Loam soil that I know of in the Central Valley.

The West Units were surprisingly free of many common woody invasive species: Only a few salt-cedars were present, Arundo existed only as two patches on Vierra, (and was spreading north after the 1997 flood), Himalayan blackberry was discovered only as small patches at Lara, and Star-thistle was not on the Refuge (but it was at the East Stanislaus Irrigation District gate, as were the only ground squirrels).

I carried out what we term as a site analysis. I reviewed historic photos of former land uses and former flood events; we excavated soil pits across the Refuge to evaluate soil textures and depth to water table, and I interviewed local residents, including Ed Hagemann who toured me around his former holdings and explained how he developed and managed his farm. I compiled a Pre-Restoration Plan for the West units that explained the current ecological conditions on the Refuge and recommended where and how riparian restoration could be implemented, including plant species associations and the placement of wetlands. The Pre-restoration Plan was attached to a funding proposal that was submitted by the Refuge to CalFed for funding.

Meanwhile wildlife targets for the restoration of the west units were established: 1. Recovery of the Endangered Riparian Brush Rabbit (RBR). (The Endangered Species Recovery Program at CSU Stanislaus designated the San Joaquin River NWR as the primary location to establish new populations of the RBR. The RBR is currently the primary driver of restoration designs at the Refuge). 2. Establishing habitat for the Valley Elderberry Longhorn Beetle, and 3. Conservation of Californian riparian bird species and their habitat as identified by the national Partners in Fight Program.

In preparation for the restoration process, Refuge staff collected cottonwood, arroyo willow, and black willow to establish a cuttings nursery for the future work that would require many thousands of stem cuttings of these species. At that time, there was only one arroyo willow on the Refuge (a large old individual at the relic meadow site); there were few cottonwoods on the Refuge likely due to beaver activity.

In 2002 River Partners received funding from Cal Fed to restore 777 acres to riparian habitat (San Joaquin A&B). Planting of the first half was carried out in the Fall, with the remainder planted in the spring of 2003. Plant associations were designed and located based upon soil texture and depth to water table and with a conscious regard for what the structure of the vegetation (habitat) would be in the future after all plant species had reached mature height and canopy spread. During this time, we planted the first RBR flood-refuge “Bunny Mound” adjacent the field H20 at the first “release site” for captive-bred RBRs onto the Refuge.

Test-plots were established in 2003 to test the feasibility of planting native understory species into the larger restoration project. Mugwort, Gumplant, and Creeping rye grass proved successful in becoming established from seed within the context of the management practices – irrigation timing, weed control mowing – as carried out for the woody species. The test plots proved successful.

Subsequently, in 2004, the three herbaceous species were seeded across the entire 777 acres where they established a dense, weed-proof cover. The seed from the mugwort, gumplant, and Creeping rye grass were all collected from on the Refuge. The discovery of a patch of Creeping rye grass (sw Lara) that was producing abundant seed was an unusual and fortuitous find. This allowed for us to restore the native grass using seeds that we were confident were adapted to the ecological conditions on the Refuge.

However, in July of that year a wildfire (The Pelican Fire) burned from Hwy 132 to Grayson, nearly five and a half miles. The restoration fields did not burn as they were being irrigated at the time. The first black-tailed deer ever spotted on the Refuge was revealed shortly after the fire – it was alive and healthy. Most RBR that were radio-collared also survived. That Fall we used Burn Area Emergency Response (BAER) funds to plant native creeping rye grass on the burned portion of the Christman Island Unit.

In 2005 River Partners received funding for restoration of 560 acres on the Vierra Unit, approximately one-third of which is seasonal wetland. That same year we carried out the first levee planting along H20 for Riparian Brush Rabbit flood refugia. The reference site for the levee plantings was a patch of vegetation growing on the east side of the levee on the Vierra unit (Field V8). This patch of rose, blackberry, and sandbar willow had been present during the 1997 floods and was a healthy stand of plants, despite growing on a steep slope well above the floodplain surface.

In early June 2005 a bird monitor spotted a pair of nesting Least Bells Vireo (LBVI) on the refuge, a federally endangered species that had not been seen in the San Joaquin valley for 60 years. The same pair was discovered nesting the following year as well.

Gray fox in a stand of willows, planted by River Partners. Photo by River Partners staff.

In 2006 the Refuge experienced a Long Duration Flood (LDF), the type that begins in January, increases in March and drains off the Refuge in July (for a total of 15-17 weeks in many places). The flood demonstrated the need for flood refugia for RBR and all other terrestrial species. We also learned how each species of plant responded to the LDF (see detailed report in RP library): species that could not tolerate the LDF and died out completely included Elderberry and Coyote Brush; species that survived close to 100 percent included Black willow, Sandbar willow, Oregon ash, Fremont cottonwood, Valley oak. Subsequently, the Vierra unit was redesigned and LDF tolerant species were planted.

In 2006 we also began our levee plantings, covering 9,000 feet of levee sides to function as flood refugia for RBR (funding provided by the Regional Water Quality Control Board water quality fines from two local cities and one manufacturer). The levee plant associations are composed of shrub species only, including rose, blackberry, coyote brush, elderberry; sandbar willow was planted along the base of the levee as a wind-wave buffer; understory species-mugwort and gumplant were also included.

The earlier success of the Bunny Mounds (flood refugia) led River Partners to build an additional 27 on Vierra and Christman island in 2007. These were constructed by belly-scrapers and dozers along the edges of the wetland in Vierra and at a few places on Christman Island. They are about ten feet higher than the surrounding floodplain. They are planted with shrub species and the base of each mound is surrounded with “green-rip-rap” – a dense planting of sandbar willow that will not only provide habitat, but will also protect the mound from erosion by waves during flood events.

That year we planted the Hagemann I, the unit that includes the field with the highest elevation on the Refuge –planted with nearly all shrubs (ten percent trees) and with the addition of a new species – quailbrush, Atriplex lentiformis due to its ability to tolerate drought and its reputation as dense cover for wildlife. (Quailbush is native to the Kern River area at the head of the San Joaquin Valley).

This aerial photo along the San Joaquin River, taken in 2011, shows River Partners’ newer plantings (2007) in the foreground alongside older plantings (2002) in the background, which after 10 years have become a fully functioning ecosystem.

Over the subsequent five years we have continued our restoration work on the Refuge, extending our plantings to other units with designs that include additional species trials. We continue to build more Bunny Mounds, and have completed 4.5 miles of plantings on both sides of Refuge levees. In 2011, with funding from ERFA (Ecosystem Restoration & Floodwater Attenuation Project, San Joaquin River), we constructed a flood relief weir to manage floodwaters entering the Refuge. And this March, with a grant from ERFA, we began restoration plantings on Hagemann III. Obviously, our work on the Refuge is far from over.

Grants from partners, such as ERFA, Cal Fed, Department of Water Resources and others have enabled River Partners to carry out its riparian restoration work on the San Joaquin River National Wildlife Refuge. Our work on the Refuge has benefited the state and people of California in many ways, including reducing flood risk on adjacent agricultural properties, enhancing the ecosystem by restoring riparian habitat, increasing groundwater recharge, improving public access to the San Joaquin River and reducing operation and maintenance costs for flood control facilities on the San Joaquin River.

The above article originally appeared in the Winter 2012 issue of the River Partners Journal.