DOI: 10.6073/pasta/e2d248fcfaa8a1668b602d11984a5a2c
title: Interagency Ecological Program: Fish catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2023.

description: 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. Collect baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance. 2. Analyze and communicate Yolo Bypass data with stakeholders and the scientific and management communities to address pertinent management-related questions. 3. Provide technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. The YBFMP operates a rotary screw trap and fyke trap and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. Only juvenile and adult fish catch with associated water quality are presented in this dataset. The rotary screw trap sampling objectives are to: (1) examine species abundance and life stage of juvenile outmigrants and resident small-bodied fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, and (3) examine the effect of physical and environmental conditions on these patterns. The fyke trap sampling objectives are to: (1) examine abundance of migrating and resident adult fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, especially with regard to anadromous species, (3) examine the effect of physical and environmental conditions on these patterns, and (4) provide data on the timing and duration of species captured in the Yolo Bypass for comparison to those captured in other Sacramento Valley tributaries. The beach seine surveys are conducted in the Yolo Bypass’s perennial channel (Toe Drain), inundated floodplain, disconnected inundated ponds, and perennial ponds. The objectives of Toe Drain and inundated floodplain beach seine sampling are: (1) to examine species abundance and composition in different water year types and inundation conditions, (2) to spatially compare fish abundance and diversity in the Yolo Bypass, and (3) to estimate growth rates and densities of salmon in the Yolo Bypass versus the Sacramento River. The objectives for beach seine sampling in disconnected inundated ponds are: (1) measure the diversity and abundance of fish species stranded in ponds located in different regions and habitats, (2) to compare relative densities of fish before and after floodplain drainage, (3) to examine the sources of fish mortality in ponds including temperature, desiccation and predation, (4) to develop long-term annual Yolo Bypass stranding indices for reference locations, and (5) to examine relationships between annual stranding indices and physical variables such as hydrology and temperature. The objectives for seine sampling in the perennial ponds are: (1) to examine seasonal fish species abundance and diversity in the Yolo Bypass versus the Sacramento River and (2) to examine species abundance and composition in different water year types. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts. YBFMP staff also conduct analyses of YBFMP monitoring data to address pertinent management related questions as identified by IEP. The Yolo Bypass has been identified as a high restoration priority by the National Marine Fisheries Service and US Fish and Wildlife Service Biological Opinions for Delta Smelt, Winter and Spring-run Chinook salmon and by California EcoRestore. The YBFMP informs the restoration actions that are mandated or recommended in these plans and provides critical baseline data on the ecology of the bypass and how it interacts with the broader San Francisco Estuary. Key findings include: (1) YB is a major factor regulating year class strength of splittail (Sommer et al. 1997; Feyrer et al. 2006; Sommer et al. 2007a); (2) YB is a key migration corridor for adult fish of several listed species and sport fish (Harrell and Sommer 2003; Johnston et al. 2020); (3) YB is one of the most important regional rearing areas for juvenile Chinook salmon (Sommer et al. 2001a; 2005; Goertler et al. 2017, 2018; Sommer et al. 2020); (4) YB provides habitat for endangered Delta Smelt and its congeners (Mahardja et al. 2019; Davis et al. 2022), (5) and YB is a source of phytoplankton to the food web of the San Francisco Estuary (Jassby and Cloern 2000; Schemel et al. 2003; Sommer et al. 2004a; Frantzich et al. 2018).