This data is an integration of raw logger data as well as relevant California Data Exchange Center (CDEC) data (Pien et al. 2020, hourly) and water quality data collected during the Yolo Bypass Fish Monitoring Program’s (YBFMP) fish collection (Pien and Kwan 2022) to produce a daily water temperature dataset for the Yolo Bypass and Sacramento River at Sherwood Harbor and Rio Vista Bridge. The raw YBFMP’s water temperature data was collected by loggers attached to the rotary screw trap (STTD) and Sherwood Harbor (SHR). Logger data ranged from daily means (1998) to a fifteen-minute collection interval (2013-2017 for the Yolo Bypass, 2009-2019 for Sherwood Harbor). A daily mean, maximum, minimum, standard deviation and coefficient of variation in water temperature was produced as well as columns for sample size (n, number of measurements per day), method (data collection or estimation), category, length (number of consecutive missing dates) and site. Daily water temperature data for the full extent of the YBFMP’s fish collection is valuable for a variety of purposes. For example, variation in water temperature during inundation and comparisons between temperatures in the Sacramento River and Yolo Bypass have been used as metrics of habitat complexity and linked to life history diversity in salmon (Goertler et al. 2017).