The establishment of water quality prediction models is vital for aquatic ecosystems analysis. The traditional methods of water quality index (WQI) analysis are time-consuming and associated with a high degree of errors. These days, the application of artificial intelligence (AI) based models are trending for capturing nonlinear and complex processes. Therefore, the present study was conducted to predict the WQI in the Kinta River, Malaysia by employing the hybrid AI model i.e., GA-EANN (genetic algorithm-emotional artificial neural network). The extreme gradient boosting (XGB) and neuro-sensitivity analysis (NSA) approaches were utilized for feature extraction, and six different model combinations were derived to examine the relationship among the WQI with water quality (WQ) variables. The efficacy of the proposed hybrid GA-EANN model was evaluated against the backpropagation neural network (BPNN) and multilinear regression (MLR) models during calibration, and validation periods based on Nash–Sutcliffeefficiency (NSE), mean square error (MSE), root mean square error (RMSE), mean absolute percentage error (MAPE), and correlation coefficient (CC) indicators. According to results of appraisal the hybrid GA-EANN model produced better outcomes (NSE = 0.9233/ 0.9018, MSE = 10.5195/ 9.7889 mg/L, RMSE = 3.2434/ 3.1287 mg/L, MAPE = 3.8032/ 3.0348 mg/L, CC = 0.9609/ 0.9496) in calibration/ validation phases than BPNN and MLR models. In addition, the results indicate the better performance and suitability of the hybrid GA-EANN model with five input parameters in predicting the WQI for the study site.