The impact of climate change on the oxygen saturation content of the world’s surface waters is a significant topic for future water quality in a warming environment. While increasing river water temperatures (RWTs) with climate change signals have been the subject of several recent research, how climate change affects Dissolved Oxygen (DO) saturation levels have not been intensively studied. This study examined the direct effect of rising RWTs on saturated DO concentrations. For this, a hybrid deep learning model using Long Short-Term Memory integrated with k-nearest neighbor bootstrap resampling algorithm is developed for RWT prediction addressing sparse spatiotemporal RWT data for seven major polluted river catchments of India at a monthly scale. The summer RWT increase for Tunga-Bhadra, Sabarmati, Musi, Ganga, and Narmada basins are predicted as 3.1, 3.8, 5.8, 7.3, 7.8 °C, respectively, for 2071–2100 with ensemble of NASA Earth Exchange Global Daily Downscaled Projections of air temperature with Representative Concentration Pathway 8.5 scenario. The RWT increases up to7 °C for summer, reaching close to 35 °C, and decreases DO saturation capacity by 2–12% for 2071–2100. Overall, for every 1 °C RWT increase, there will be about 2.3% decrease in DO saturation level concentrations over Indian catchments under climate signals.