In recent decades, various conventional techniques have been formulated around the world to evaluate the overall water quality (WQ) at particular locations. In the present study, back propagation neural network (BPNN) and adaptive neuro-fuzzy inference system (ANFIS), support vector regression (SVR), and one multilinear regression (MLR) are considered for the prediction of water quality index (WQI) at three stations, namely Nizamuddin, Palla, and Udi (Chambal), across the Yamuna River, India. The nonlinear ensemble technique was proposed using the neural network ensemble (NNE) approach to improve the performance accuracy of the single models. The observed WQ parameters were provided by the Central Pollution Control Board (CPCB) including dissolved oxygen (DO), pH, biological oxygen demand (BOD), ammonia (NH3), temperature (T), and WQI. The performance of the models was evaluated by various statistical indices. The obtained results indicated the feasibility of the developed data intelligence models for predicting the WQI at the three stations with the superior modelling results of the NNE. The results also showed that the minimum values for root mean square (RMS) varied between 0.1213 and 0.4107, 0.003 and 0.0367, and 0.002 and 0.0272 for Nizamuddin, Palla, and Udi (Chambal), respectively. ANFIS-M3, BPNN-M4, and BPNN-M3 improved the performance with regard to an absolute error by 41%, 4%, and 3%, over other models for Nizamuddin, Palla, and Udi (Chambal) stations, respectively. The predictive comparison demonstrated that NNE proved to be effective and can therefore serve as a reliable prediction approach. The inferences of this paper would be of interest to policymakers in terms of WQ for establishing sustainable management strategies of water resources.