The Yolo Bypass Fish Monitoring Program

The California Department of Water Resources (DWR), with support from the Interagency Ecological Program (IEP), has operated the Yolo Bypass Fish Monitoring Program (YBFMP) since 1998. The program collects baseline data on hydrology, water quality, lower trophic organisms, and juvenile and adult fish. The YBFMP provides critical information regarding the significance of seasonal floodplain habitat to native fishes. 

Early exploration of the bypass was aimed at understanding the extent fish stranding and mortality in the bypass when floodwater receded. Contrary to the expectation that the bypass was a death-trap for fish, researchers began to discover that, not only did most fish find their way off the floodplain, but that the Yolo Bypass provided a host of critical benefits (Sommer et al. 2001a). Key findings include:

• The Yolo Bypass provides key spawning habitat for Sacramento Splittail, especially when flooded (Sommer et al. 1997, 2002).
• Splittail are obligate floodplain spawners, meaning they need flooded vegetation as a substrate to successfully reproduce (Moyle et al. 2007) and the amount of inundated floodplain habitat is one of the most important factors explaining annual production of age-0 Splittail (Feyrer et al. 2006).
• The opportunity for juvenile Chinook Salmon to rear in the Yolo Bypass floodplain leads to higher growth rates and improved survival (Sommer et al. 2001b, 2005).
• Improved access to floodplain habitat can help expand the life history portfolio for salmon (Takata et al. 2017) and support size variation (Goertler et al. 2018a).
• Different native fish use the bypass at different times, highlighting the importance of diversity in flood timing (Kwan et al. 2018).
• The Yolo Bypass may be capable of providing refuge habitat for Delta Smelt during drought periods (Mahardja et al. 2019).

• Water residence in the bypass can trigger productive phytoplankton blooms which form the base of the food web for many fish species (Schemel et al. 2004; Lehman et al 2008; Frantzich et al. 2018)
• One major food resource is the initial pulse of invertebrates, which mainly consists of Chironomidae, which emerge from floodplain sediments (Benigno et al. 2008).
• Additionally, water held on the floodplain and in agricultural rice fields can support dense zooplankton communities which provide ample food for rearing juvenile salmon (Corline et al. 2017; Katz et al. 2017; Sommer et al. 2020).
• Though hydrologic conditions change dominant prey types, juvenile salmon can find preferred, calorically valuable prey in the bypass in drought and flood periods (Goertler et al. 2018b).

• The Yolo Bypass is a complex migratory corridor for adult sturgeon and salmon. When the bypass is flooded, these fish can migrate up the Yolo Bypass and connect with the Sacramento River. When disconnected, these species must be rescued or exit the bypass in the south to continue migration.
• Partner studies have found exit rates of salmon and sturgeon differ by species (Johnston et al. 2020) and that removing agricultural barriers, operating a rescue facility (EcoRestore, a), and creating an adult fish passage "notch" in the Fremont Weir can help improve adult survival (EcoRestore, b).
• White Catfish, Channel Catfish, and Common Carp are the most common invasive species, with Sacramento Splittail, Sacramento Sucker, and White Sturgeon historically comprising the most common native species. Different species associate with different environmental variables (Sommer et al. 2014).

The Yolo Bypass, located west of Sacramento, CA, is the largest remnant floodplain of the Sacramento River. Historically, the Yolo Basin was a nearly 80,000 acre wetland ecosystem which served as a home or stopover habitat for a variety of birds, fish, and wildlife. However, as cities and towns grew up around the basin, there came a need for some kind of flood control infrastructure.

The Army Corps of Engineers responded by building levees around a designated floodplain and constructing a two mile long earthern berm along the Sacramento River. This berm, known as the Fremont Weir, was completed in 1924 and is designed to overtop when water levels in the Sacramento River exceed 32 ft. When the river exceeds this height, excess water spills over the weir and into the Yolo Bypass.

The Sacramento Weir, built in 1916, is a 1,920 ft. long, manually operated weir located downstream of Fremont Weir. The weir consists of 48 gates which can be opened in stages once the river elevation reaches 29.8 ft. It is usually only operated during extremely wet years (last was in 2017) but even when unopened higher river levels will lead to some seepage through the gates, allowing for varying levels of connectivity to the bypass.

During non-flooding periods, the bypass serves as a home for local agriculture, mostly rice farming, private duck clubs, livestock grazing, and the Yolo Bypass Wildlife Preserve. The southern bypass also connects to the tidal portion of the Sacramento - San Joaquin Delta, where tidal restorations projects have been established or are being planned. The presence of agriculture, duck clubs, and the preserve mean that even when the Sacramento River isn't flooding over the weirs, there is still a fair amount of water being held and moved across the landscape. Most of this water ends up in the Toe Drain canal (also sometimes called Prospect Slough or the Tule Canal), which transports it south into the Delta.

Human alteration of the Yolo Bypass have changed it substantially from it's historic state. However, the bypass is still subject to varying levels of bypass flooding through agriculture, duck clubs, tidal wetlands, local runoff, and occasional weir overtopping. As such, it provides many of the same key ecological services as historic floodplains, which benefit fish (and wildlife) species.

Currently, an exciting project is underway on the eastern end of the Fremont Weir that will change the frequency, duration, and timing of bypass inundation in the future:

The Yolo Bypass Salmonid Habitat Restoration and Fish Passage (Big Notch) Project will have operable gates to divert river water into the bypass even when the river stage is not high enough to overtop the main weir. It is permitted to operate between November 1st to March 15th. The goals of the project are to increase floodplain rearing habitat for juvenile salmonids and provide adult fish passage for adult salmonids and sturgeon back to the river.

The Yolo Bypass Fish Monitoring Program (YBFMP) samples juvenile and adult fish, lower trophic organisms, chlorophyll, and water quality at various locations throughout the Yolo Bypass and in the Sacramento River. The program's methods are detailed below:

Beach seine sampling is conducted in shallow shoals and seasonally flooded areas to examine stranding patterns, species abundance, and species composition across different water year types, in different regions, and at different points during the flood cycle. Sampling began in 1998 and currently takes place biweekly year-round and weekly during flooding periods. The seine used is 25’ x 4’ with a 4’ bag with 1/8” mesh. Due to the steepness of the levee banks, modified beach seine hauls are performed parallel to the shoreline as opposed to netting perpendicular to the shoreline.

The fyke trap sampling is designed to examine adult fish species composition and the timing and duration of fish migration through the Yolo Bypass. Sampling began in 1999 and occurs Monday-Friday from October through June, the period over which most adult fish species migrate. The fyke trap used is 10’ in diameter and 24’ in length. 

Rotary screw trap sampling examines the species composition, relative abundance, and emigration timing of fish moving out of the Yolo Bypass floodplain. The 8’ diameter trap tends to sample smaller species, juvenile salmonids and juveniles of other species. Sampling began in 1998 and occurs Monday-Friday from January through June, the period over which most juvenile fishes move out of the floodplain. The site is tidally influenced which presents a unique situation for typical screw trap operations. 

Zooplankton sampling evaluates and compares the seasonal composition and abundance of zooplankton in the Yolo Bypass floodplain with the mainstem Sacramento River. This monitoring also provides data on food availability for fishes since zooplankton are an important diet component for many species and life-stages. Sampling began in 1999 and currently occurs biweekly, year-round. This sampling utilizes a 50-micron mesh conical plankton net and a 150-micron mesh, 0.5m in diameter and 2m long, conical plankton net. 

This monitoring targets aquatic and terrestrial insects and other surface-oriented invertebrates to examine and compare composition and abundance between the Yolo Bypass and Sacramento River. Aquatic and terrestrial insects are an important component in the diet of juvenile and adult fishes, including two important natives: juvenile Chinook Salmon and Sacramento Splittail. Sampling has occurred since 1998 and currently runs biweekly, year-round. This sampling utilizes a 500-micron mesh, 0.46m (mouth width) x 0.3m (mouth height) x 0.91m (net length), drift net. 

The collection of fish larvae and eggs measures seasonal variation in densities and species assemblages within the Yolo Bypass. Sampling began in 1999 and occurs biweekly from January through July currently, and used to occur year-round. The net used consists of 500-micron mesh and is 0.65m in diameter and 2m long.

Discrete water quality measurements are taken at all sampling locations and include: water temperature, secchi, dissolved oxygen, specific conductivity, electric conductivity, turbidity, and pH. Multiparameter sondes located at Lisbon Weir and the screw trap site also collect year-round 15 minute interval water quality data. Every other week, concurrent with lower trophic sampling, water at Sherwood Harbor, Lisbon Weir, and the screw trap site is sampled, filtered, and analyzed at the DWR Bryte Laboratory.

Chlorophyll sampling compares seasonal and annual variation in primary production within the Sacramento River and the Yolo Bypass. Sampling began in 2001 and has occurred biweekly, year-round, since 2011 at Sherwood Harbor, Lisbon Weir, and the screw trap site. Phytoplankton is also collected and analyzed by contractors.

To see more photos of our program in action, click the button below:

You can find our website, which includes a list of staff, publications, internal reviews, links to YBFMP open-access data, and other helpful resources, by clicking the button below:

Also, check out some our our public and youth outreach, including our Frontiers for Young Minds article about floodplain benefits!

Our IEP blog post describing our drift intervebrate dataset:

And our "Water Wednesday" talk about some of the Yolo Bypass's notable native fishes: