Neural network (NN) models have gained much attention for river flow forecasting because of their ability to map complex non-linearities. However, the selection of appropriate length of training datasets is crucial and the uncertainty in predictions of the trained NNs with new datasets is a crucial problem. In this study, self-organising maps (SOM) are used to classify the datasets homogeneously and the performance of four types of NN models developed for daily discharge predictions – namely traditional NN, wavelet-based NN (WNN), bootstrap-based NN (BNN) and wavelet-bootstrap-based NN (WBNN) – is analysed for their applicability cluster-wise. SOM classified the training datasets into three clusters (i.e. cluster I, II and III) and the trained SOM is then used to assign testing datasets into these three clusters. Simulation studies show that the WBNN model performs better for the entire testing dataset as well as for values in clusters I and III; for cluster II the performance of BNN model is better compared with others for a 1-day lead time forecasting. Overall, it is found that the proposed methodology can enhance the accuracy and reliability of river flow forecasting.