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The San Francisco Estuary and Sacramento–San Joaquin River Delta (Bay Delta) is a highly sensitive and critical habitat for the Delta Smelt, an endangered endemic fish, with water temperature being a key determinant of habitat suitability. This study investigates the relationship between open water surface and subsurface conditions from spaceborne thermal measurements (ECOsystem Spaceborne Thermal Radiometer Experiment on Space Station (ECOSTRESS) and Landsat-8) and in situ sensor data from the California Data Exchange Center (CDEC) to produce estimates of spatially continuous bulk temperature in the Bay Delta. We found that ECOSTRESS and Landsat-8 surface temperature measurements are well-correlated with bulk water temperatures ($N =236$ and $r = 0.907$ and $N = 226$ and $r = 0.976$ , respectively). For the ECOSTRESS-in situ comparison, accounting for time of day improved the correlation between surface and subsurface conditions ($r = 0.946$ , 0.881, and 0.944 for morning, midday, and evening, respectively). We found that ECOSTRESS surface temperatures were warmer than bulk temperatures in the midday period (2 °C peak at 2 P.M.) and cooler in the morning and evening periods (−1°C peak at 6 A.M.). We also found that a simple harmonic regression model can capture the diurnal variability of the skin effect to predict bulk water temperature (root-mean-square error (RMSE) = 0.809°C). With ECOSTRESS, we found that across the Bay Delta, including open waters and pelagic bays, temperature conditions causing stress and mortality for the Delta Smelt were persistent throughout the day during summer months. ECOSTRESS is a unique dataset capable of informing conservation efforts in the Bay Delta. [ABSTRACT FROM AUTHOR]