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This study uses Landsat 5, 7, and 8 level 2 collection 2 surface temperature to examine habitat suitability conditions spanning 1985-2019, relative to the thermal tolerance of the endemic and endangered delta smelt ( Hypomesus transpacificus ) and two non-native fish, the largemouth bass ( Micropterus salmoides ) and Mississippi silverside ( Menidia beryllina ) in the upper San Francisco Estuary. This product was validated using thermal radiometer data collected from 2008 to 2019 from a validation site on a platform in the Salton Sea (RMSE = 0.78 °C, r = 0.99, R 2 = 0.99, p < 0.01, and n = 237). Thermally unsuitable habitat, indicated by annual maximum water surface temperatures exceeding critical thermal maximum temperatures for each species, increased by 1.5 km 2 yr -1 for the delta smelt with an inverse relationship to the delta smelt abundance index from the California Department of Fish and Wildlife ( r = -0.44, R 2 = 0.2, p < 0.01). Quantile and Theil-Sen regression showed that the delta smelt are unable to thrive when the thermally unsuitable habitat exceeds 107 km 2 . Warming waters in the San Francisco Estuary are reducing the available habitat for the delta smelt.2 yr -1 . Warming waters in the San Francisco Estuary are reducing the available habitat for the delta smelt.