Understanding the riverine thermal regimes is challenging due to sparse spatiotemporal data of river water temperatures (RWTs). The development of systematic models combined with machine learning models under data‐limited context has not been intensively studied for the prediction of RWT. The present study developed hybrid models using long short‐term memory (LSTM), integrated with (a) k‐nearest neighbor (k‐NN) bootstrap resampling algorithms (kNN‐LSTM) to address the data limitations of RWT prediction and (b) discrete wavelet transform (WT) approach (WT‐LSTM) to address the time–frequency localized features of RWT prediction. The study assessed the climate change impacts on RWT using an ensemble of National Aeronautics Space Administration Earth Exchange Global Daily Downscaled Projections of air temperature with Representative Concentration Pathway scenarios 4.5 and 8.5 for seven major polluted river catchments of India. The hybrid kNN‐LSTM has effectively predicted RWT at monthly time scales under data limitations and outperformed the standalone LSTM, WT‐LSTM, and hybrid three‐parameter version air2stream models. The RWT increase for Tunga‐Bhadra, Musi, Ganga, and Narmada basins is predicted as 3.0, 4.0, 4.6, and 4.7°C, respectively, for 2071–2100.