Largely supported by the Interagency Ecological Program (IEP), the California Department of Water Resources (DWR) has operated a fisheries and invertebrate monitoring program in the Yolo Bypass since 1998. The main objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to collect baseline data on lower trophic levels (phytoplankton, zooplankton and insect drift), juvenile and adult fish, hydrology, and water quality parameters. As the Yolo Bypass has been identified as a high restoration priority by the US Fish and Wildlife Service and National Marine Fisheries Service biological opinions for Delta Smelt (Hypomesus transpacificus) and winter and spring-run Chinook Salmon (Oncorhynchus tshawytscha), and by California EcoRestore, these baseline data are critical for evaluating success of future restoration projects. In addition, the data have already served to increase our understanding of the role of the Yolo Bypass in the life history of native fishes, and its ecological function in the San Francisco Estuary. 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. Since 2011, samples have been 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 (1) Sacramento River channel, and (2) the Yolo Bypass, the river’s seasonal floodplain. Key findings to date: (1) Chinook Salmon sampled in the floodplain had diets comprised of 90% Dipterans and zooplankton, with Chironomidae being the dominant Diptera family (Sommer et al., 2001), (2)The floodplain of the Yolo Bypass contains significantly higher densities of Diptera (Diptera densities being 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) A major portion of the diet of juvenile Sacramento Splittail are chironomid larvae (Kurth and Nobriga 2001, Moyle et al. 2004, Sommer et al. 2007), and (4) The Yolo Bypass was the site of the recent discovery of a new aestivating and winter emerging chironomid; Hydrobaenus saetheri (Cranston et al. 2007).