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Home » News/Events » The Journal » Vol. 14 Issue 1 » When Flood Safety and Wildlife Recovery Coincide or Collide

When Flood Safety and Wildlife Recovery Coincide or Collide: More Lessons Learned on the San Joaquin River

  • Heyo Tjarks, Central Valley Restoration Ecologist
  • Jeff Holt, Central Valley Restoration Biologist
  • Maggie Boberg, Central Valley Regional Director

Although it may look under-whelming, this levee breach has saved millions of dollars of investment in habitat restoration from damaging conditions, and is the only such example in California of a purposeful breach providing floodplain habitat connectivity to benefit people and wildlife. Photo credit: USFWS.

Over the years, we have embraced the core value that quality ecological restoration requires design considering all types of future site conditions, ranging from disturbed to protected, frequently burned to frozen, and severe drought to prolonged flood. Given California’s status of “extreme drought conditions” over the past four years, it was difficult to imagine how our more recent restoration designs would be impacted by high waters. This past winter, flooding on the San Joaquin River provided a spotlight for management decisions made and designs implemented over the past decade at the San Joaquin River National Wildlife Refuge (Refuge). We have learned a lot of lessons that will guide future projects as we continue to attempt to account for the suite of possible future conditions. Here is what we learned:

On February 15, 2017, California had already experienced several months of steady rainfall; flows at the Vernalis flow gauging station (a few miles downstream from the Refuge) were just reaching flood stage and were projected to continue rising over the next few days. But then, something happened.

The earthen banks of the West Stanislaus Irrigation District’s (WSID) main canal breached, leaving a 100-foot wide, 10-foot deep gap; through which river water began pouring into the 1,500-acre Refuge at an estimated rate of 2,000 cubic feet per second. Water accumulated on the dry side of the levees to the north and south of the breach, submerging nearly 3,000 acres of restored riparian and seasonal wetland habitat that was funded through $25 million in state and federal grants.

By March 3, the water level in the Refuge was over 10 feet deep. Fortunately, the landowner, the US Fish and Wildlife Service, had obtained an emergency allowance from the Army Corps of Engineers and California’s Central Valley Flood Protection Board to breach the downstream levee holding water back. Floodwater flowed out of the Refuge through the emergency levee breach, eventually draining back to the San Joaquin River channel. This drainage reduces the threat of fish stranding behind the levee, and promotes water circulation that protects the restored vegetation from damage. Water depth in the Refuge remained high (6-8 feet in places) until July.

View of the swollen San Joaquin River as it meanders past River Partners’ most recent acquisition: the 285-acre Grayson Ranch (foreground), the 2,000-acre Dos Rios Ranch (background), and the 3,000-acre West Unit of the San Joaquin River National Wildlife Refuge (restoration visible to the left side of the photo).

The events of February 15th – March 3rd provide a real-world example of “transitory flood storage” or the idea that floodplains can be used to reduce flood stage locally by accepting a slug of water quickly. When the WSID canal bank breached, water experts were projecting flows continually increasing in the river channel, reaching a peak stage within the next few days. Instead of reaching peak flood flows, however, up to 20,000 acre-feet of water flowed onto the Refuge. This was enough “storage” to keep the San Joaquin River from reaching peak stage for over 24 hours at the Vernalis gauge station and 12 hours at the Mossdale Bridge gauge station (over 25 miles downstream). This extra time can make a big difference for evacuations and emergency responders.

Data from the Vernalis gauging station shows river stages observed (blue) and forecast (green) as related to the official flood stage (red). The sizable dip in river stage (well below official flood stage) noted in February 16 is the direct result of inundation of the floodplain at the Refuge. With additional development of transitory floodwater storage, we could see a tremendous improvement in flood management for millions of residents in the South Delta and Stockton.

However, two issues arose that are of serious concern for terrestrial wildlife: The rapid flooding caused mortality – drowning wildlife immediately; and the long duration flood also caused mortality, by eliminating food plants for flood survivors. This rapid flooding happens much faster than wildlife are able to respond to. A bunny simply can’t outrun a flood rush that large. Creating numerous high water “refugia” across the floodplain for terrestrial species is one design concept that we’ve incorporated into floodplain restoration here to help with the problem. And they have mostly worked. Following floods in 2006 versus 2011, we saw a significantly faster post-flood repopulation of the habitat with rabbits once elevated refugia were present. For a more detailed description of the workings of the elevated refugia, see the next section Impacts to Wildlife.

Map of the region. Note the confluence of the Tuolumne River with the San Joaquin River. This important junction complicates flood management for the area as the operations of three large dams must be coordinated to reach flow targets downstream. Projects that provide transitory floodplain storage can provide dam operators with flexibility in their management decisions, potentially reducing flood damages downstream while also potentially saving more water behind the dam for later use.

River Partners sees this example as an opportunity. Just across the San Joaquin River from the Refuge lies Dos Rios Ranch, with the capacity to store an additional 10,000 acre-feet of peak stage flows. We will continue working with multiple stakeholders to identify ways a levee breach can be engineered to open at the exact moment when peak flows are coming down the river in order to protect downstream communities, while incorporating the necessary habitat components (elevated refugia, drainage swales and breaches) that protect wildlife populations too.

Impacts to Wildlife

The “Godzilla El Nino of 2016” ended with a dull thud in the Central Valley, producing above average precipitation, but nothing near the torrential rains predicted by most climate models. By all accounts this winter wasn’t supposed to be anything remarkable, but reservoirs filled to capacity, rivers inundated floodplains, and snow packs hit historic highs.

One of the released rabbits in the San Joaquin River Wildlife Refuge (west of Modesto, along the San Joaquin River) in 2005.

While all of this water is great for a drought-weary state, it can spell disaster for many of the terrestrial inhabitants of the floodplain. One such species is the Riparian Brush Rabbit (Sylvilagus bachmani riparius), found only on the Valley floor. Their historic range stretched as far south as possibly the Merced River and north into the San Joaquin Delta. Currently their populations are confined to small fragments of habitat in the south delta near the town of Lathrop, Caswell State Park along the Stanislaus River, and the Refuge.

In the late 1990’s, the brush rabbit was thought to be on a path to extinction, numbering as few as 300 in the wild, so state and federal agencies began working with the Endangered Species Recovery Program (ESRP), based out of California State University Stanislaus, on captive propagation and reintroduction efforts. Native rabbits were captured and placed in enclosures with the intention of releasing their offspring into the wild. The Refuge was the chosen location for these captive born offspring, having both the appropriate location and habitat needs of the species. By 2012, approximately 1,500 brush rabbits had been released at the Refuge at several locations with the appropriate habitat. The population has endured both fires and floods, two natural disturbances associated with riparian habitat, and continue to thrive.

River Partners has been working at the Refuge since the early 2000’s as well, restoring over 2,500 acres of riparian habitat. During that time, we’ve documented the effects of major flood events that left restored fields inundated for months and brush rabbits stranded on sparsely vegetated levees.

With each flood event there are so many opportunities to learn. In the flooding that occurred in late 2005 and early 2006, brush rabbits were able to make it to high ground, primarily the levees surrounding the floodplains of the Refuge, which had little useable vegetative cover. This in turn concentrated the rabbits in small fragmented patches of cover, which funneled the predators into these areas as well. These conditions had a dramatic effect on the brush rabbit, approximately 98% of the captive-bred, radio-collared rabbits perished.

After the flood event of 2006, River Partners, ESRP, and the Refuge staff began working on options for vegetating high ground, both on the floodplain and the linear levees. Mounds were constructed and vegetated near suitable habitat on the floodplain, levees were vegetated throughout a majority of the Refuge, and captive-raised brush rabbits were added into the environment. All that was needed was another flood event to see if the vegetated high ground worked. In March of 2011 the Refuge was again inundated with several feet of flood water, forcing brush rabbits to seek shelter on vegetated high ground.

Vegetated Bunny Mounds as part of the restored landscape, with vegetated levees in the foreground. Photo from 2009.

ESRP was able to visit several mounds on the floodplain to determine if brush rabbits were in fact using these recently constructed mounds to ride out the flood. Brush rabbits were documented on mounds and Refuge levees, which was a good indication that at least a few were able to survive. Unfortunately, what we learned was that due to the duration of the flood event, many of the mounds had their food resources exhausted quite rapidly. This led to over-browsing and as a result many of the rabbits died from lack of food. ESRP and the Refuge staff supplemented the food sources in an effort to keep the remaining rabbits alive, which was successful, but was not a sustainable management action for the future.

Trapping data indicated that after the 2006 flood, brush rabbits were not captured on the floodplain until the fall of 2007, even with brush rabbits being actively translocated to portions of the Refuge. But in 2011, once flood waters receded, brush rabbits were captured on the floodplain adjacent to bunny mounds, without supplemental introductions, so we know that rabbits survived the flood and repopulated the floodplain habitat naturally.

ESRP ended their breeding and reintroduction efforts in the summer of 2012 due to lack of funding, but the brush rabbit population at the Refuge seemed to be holding. Project partners are currently working on funding to continue monitoring for brush rabbits on the Refuge and surrounding habitat. River Partners is also working to secure funding to revegetate several mounds on the floodplain that have experienced negative effects of the ongoing drought. We are looking into more drought tolerant plant species, such as quail bush, in an effort to provide more long-term cover for the rabbits, as well as grasses and forbs for rabbit forage during future flood events.

The recent flooding in early 2017 seems to have put an end to the ongoing drought but it has again inundated large portions of the Refuge and surrounding floodplains. Brush rabbits were documented on several mounds on the floodplain and all of the vegetated levees but they again exhausted their food resources. The timing of this flood event, mid-January, meant that some of the annual grasses which would normally provide forage and cover had not germinated. What little forage was available was quickly eaten by the hundreds of rabbits forced onto the levees and mounds. Refuge staff and ESRP began moving rabbits to other portions of the Refuge to relieve some of the pressure for resources. For nearly three months, Refuge staff supplemented the food sources on the levees and mounds with bales of alfalfa and alfalfa pellets. This proved essential for maintaining a healthy and robust population. In a natural riparian system, this would not be necessary – the animals would simply hop up-gradient along the myriad drainages as the river slowly rose. However, if they tried now – assuming they could escape the unnaturally rapid inundation of the floodplain -- they would encounter bare levees and farm fields, making it impossible to survive. The habitat and river system in the Central Valley of California remains highly altered, necessitating these “rescue” efforts – pending provision of an adequate supply of high-water refugia.

This flood event highlights the need for further work on the constructed mounds and levees, which are providing the necessary high ground to avoid flood waters, but are falling short on providing enough food resources to survive a long-term flood. Refuge staff and River Partners staff were able to visit several mounds during early February to look at available resources and numbers of rabbits per mound. One of the interesting discoveries during this trip was the number of brush rabbits found on one of the newest mounds constructed in the Hagemann Tract of the Refuge. Translocations never occurred in that area. These newest mounds, two “super bunny berms” were designed and constructed to provide several acres of contiguous high-ground cover for rabbits that connects some of the lowest elevations of the floodplain to some of the highest. The design concept imagined rabbits fleeing the floodwaters along the tops of the super bunny berms, eventually making their way to native high ground where they could weather the duration of the flood. This spring, an abundance of riparian brush rabbits were found on each super bunny berm. Estimates are in the low hundreds, although without monitoring data, population numbers are difficult to estimate.

The presence of brush rabbits on vegetated mounds and levees offers hope for the survival of the species at the Refuge, especially in the face of more frequent and intense flooding associated with our changing climate. Vegetated high ground on the floodplain and vegetated levees were certainly critical to rabbit survival, and there is so much more to learn as the Refuge weathers our future climate cycles.

The above article originally appeared in the Fall 2017 issue of the River Partners Journal.