Reliable estimations of sediment yields are very important for investigations of river morphology and water resources management. Nowadays, soft computing methods are very helpful and famous regarding the accurate estimation of sediment loads. The present study checked the applicability of the radial M5 tree (RM5Tree) model to accurately estimate sediment yields using daily inputs of the snow cover fraction, air temperature, evapotranspiration and effective rainfall, in addition to the flow, in the Gilgit River, Upper Indus Basin (UIB) tributary, Pakistan. The results of the RM5Tree model were compared with support vector regression (SVR), artificial neural network (ANN), multivariate adaptive regression spline (MARS), M5Tree, sediment rating curve (SRC) and response surface method (RSM) models. The resulting accuracy of the models was assessed using Pearson’s correlation coefficient (R2), the root-mean-square error (RMSE) and the mean absolute percentage error (MAPE). The prediction accuracy of the RM5Tree model during the testing period was superior to the ANN, MARS, SVR, M5Tree, RSM and SRC models with the R2, RMSE and MAPE being 0.72, 0.51 tons/day and 11.99%, respectively. The RM5Tree model predicted suspended sediment peaks better, with 84.10% relative accuracy, in comparison to the MARS, ANN, SVR, M5Tree, RSM and SRC models, with 80.62, 77.86, 81.90, 80.20, 74.58 and 62.49% relative accuracies, respectively.