Interagency Ecological Program: Drift invertebrate and ichthyoplankton catch and water quality from the Sacramento River channel, and Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2024

Largely supported by the Interagency Ecological Program (IEP), California Department of Water Resources (DWR) has operated a fish monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: 1.Examine temporal and spatial patterns in species abundance, composition, and life stage of larval fishes, juvenile outmigrants, resident, and migrating adult fishes and evaluate the effect of physical and environmental conditions on these patterns. 2.Examine temporal and spatial trends in water quality, and abundance and community composition of phytoplankton and invertebrates in the Yolo Bypass. Compare primary and secondary productivity in the bypass to that in the adjacent Sacramento River. Aquatic and terrestrial insects are an important component in the diet of juvenile and adult fishes within the San Francisco Estuary, including two important native fishes: juvenile Chinook Salmon and Sacramento Splittail. The YBFMP collects drift invertebrates year-round from two sites. Currently, samples are collected biweekly (every other week) to weekly (during floodplain inundation) using a rectangular aquatic drift net that sits at the surface of the water. Invertebrates are identified and enumerated by contractors (currently EcoAnalysts, Inc.). The goals of the monitoring program are to compare the seasonal variations in densities and species trends of aquatic and terrestrial insects/non-insects within the Sacramento River channel and the Yolo Bypass, the river’s seasonal floodplain. Drift invertebrate Key findings to date include: (1) Chinook Salmon sampled in the floodplain had diets comprised of approximately 90% Diptera and zooplankton, with Chironomidae being the dominant dipteran family (Sommer et al. 2001b); (2) the floodplain of the Yolo Bypass contains significantly higher densities of Diptera (positively associated with flow) and terrestrial invertebrates than the adjacent Sacramento River (Sommer et al. 2001b; Sommer et al. 2004; Sommer et al. 2007); (3) drift invertebrate communities shift with hydrologic conditions, with flood years characterized by high abundances of chironomid-dominated Diptera and other aquatic insects, while drought years are associated with greater abundances of zooplankton and terrestrially derived invertebrates (Goertler et al. 2018); (4) a major portion of the diet of juvenile Sacramento Splittail consists of chironomid larvae (Kurth and Nobriga 2001; Moyle et al. 2004; Sommer et al. 2007); and (5) the Yolo Bypass was the site of the discovery of a new aestivating, winter-emerging chironomid, Hydrobaenus saetheri (Cranston et al. 2007). The collection of ichthyoplankton is one of multiple elements of the YBFMP. Currently, the YBFMP collects ichthyoplankton in the Yolo Bypass from January to July. Historically, ichthyoplankton were also sampled in the Sacramento River, but due to low catch, this was stopped in 2019. Sampling is conducted with a 500-micron mesh conical plankton net. Fish are identified and enumerated by contractors (currently EcoAnalysts, Inc). The initial goal of ichthyoplankton monitoring was to compare the seasonal variations in densities and species trends within the Sacramento River channel and the Yolo Bypass, the river’s seasonal floodplain (Sommer et al. 2003). The collection of ichthyoplankton samples is an important element in determining the annual presence, timing, and recruitment success of fishes utilizing the Yolo Bypass. Data on ichthyoplankton and associated water quality parameters are presented in this dataset. Key findings to date include: (1) 26 species of fish larvae were observed in the Yolo Bypass during the 20-years of monitoring (Mollie Ogaz and J. Frantzich, DWR, unpublished data), including Delta Smelt, Hypomesus transpacificus (Sommer et al 2004); (2) The native Prickly Sculpin and non-native Threadfin Shad dominated samples, contributing to over 60% of the total larval catch (Mollie Ogaz and J. Frantzich, DWR, unpublished data); (3) Native species made up a higher percent of total catch in the Yolo Bypass (22.43%) in comparison to in the Sacramento River (10.2%), and appeared earlier in the year than many non-natives (Mollie Ogaz and J. Frantzich, DWR, unpublished data); (4) Similar to other seasonal floodplains in the San Francisco Estuary, alien fishes made up a large portion of the assemblage of early life stages in the Yolo Bypass (Sommer et al 2004); (5) Water temperature and stage are the best explanatory environmental variables for larval fish abundance in the Yolo Bypass (p=0.001). Flow was not statistically significant (Mollie Ogaz and J. Frantzich, DWR, unpublished data); (6) Species richness and diversity are higher in the Yolo bypass in comparison to in the Sacramento River (Sommer et al. 2004). Cranston, P.S., G.M. Benigno, and M.C. Domingeuz. 2007. Hydrobaenus saetheri Cranston, new species, an aestivating, winter-emerging chironomid (Diptera: Chironomidae) from California. Pages 73-79 in Contributions to the Systematics and Ecology of Aquatic Diptera-A tribute to Ole A. Saether. T. Andersen, editor. The Caddis Press Goertler, Pascale, Kristopher Jones, Jeffery Cordell, Brian Schreier, Ted Sommer, Effects of Extreme Hydrologic Regimes on Juvenile Chinook Salmon Prey Resources and Diet Composition in a Large River Floodplain, Transactions of the American Fisheries Society, Volume 147, Issue 2, March 2018, Pages 287–299, https://doi.org/10.1002/tafs.10028 Kurth, R., and M. Nobriga. 2001 Food Habits of larval splittail. Interagency Ecological Program Newsletter 14 (2):40-42 Moyle, P. R. D. Baxter, T. Sommer, T. C. Foin, and S. C. Matern. 2004. Biology and Population Dynamics of Sacramento Splittail (Pogonichthys macrolepidotus) in the San Francisco Estuary: a review. San Francisco Estuary and Watershed Science [online serial]. Vol. 2, Issue 2 (May 2004), Article 3. Sommer, T.R., W.C. Harrell, A. Mueller-Solger, B. Tom, and W. Kimmerer. 2004. Effects of flow variation on channel and floodplain biota and habitats of the Sacramento River, California, USA. Aquatic Conservation: Marine and Freshwater Ecosystems 14:247-261. Sommer, T. R., M. L. Nobriga, W. C. Harrell, W. Batham, and W. J. Kimmerer. 2001. Floodplain rearing of juvenile Chinook salmon: evidence of enhanced growth and survival. Canadian Journal of Fisheries and Aquatic Sciences 58(2):325-333. Sommer, T, W. Harrell, and M. Nobriga. 2005. Habitat use and stranding risk of juvenile Chinook salmon on a seasonal floodplain. North American Journal of Fisheries Management 25:1493-1504. Sommer, T., R. Baxter, and F. Feyrer. 2007. Splittail revisited: how recent population trends and restoration activities led to the "delisting" of this native minnow. Pages 25-38 in M.J. Brouder and J.A. Scheuer, editors. Status, distribution, and conservation of freshwater fishes of western North America. American Fisheries Society Symposium 53. 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