In this paper, runoff time series of the sub-basins in a cascade form were decomposed by Wavelet Transform (WT) to extract their dynamical and multi-scale features for modeling Multi-Station (MS) rainfall-runoff (R-R) process of the Little River Watershed (LRW) in USA. A Self-Organizing Map (SOM) clustering technique was also employed to find homogeneous extracted sub-series' clusters. As a complementary feature, extraction criterion of mutual information (MI) was utilized for proper cluster agent choice to impose to the artificial intelligence (AI) models (Feed Forward Neural Network, FFNN; Extreme Learning Machine, ELM; and Least Square Support Vector Machine, LSSVM) to predict the runoff of the LRW sub-basins. The performance of wavelet-based runoff prediction was compared to the Markovian-based MS model. The proposed method not only considers the prediction of the outlet runoff but also covers predictions of interior sub-basins behavior. The outcomes showed that the proposed AI-models combined with the SOM and MI tools enhanced the MS runoff prediction efficiency up to 23% in comparison with the Markovian-based models. Nevertheless, benefit of the seasonality of the process along with reduction of dimension of the inputs could help the AI-models to consume pure information of the recorded data.