River inflow prediction plays an important role in water resources management and power-generating systems. But the noises and multi-scale nature of river inflow data adds an extra layer of complexity towards accurate predictive model. To overcome this issue, we proposed a hybrid model, Variational Mode Decomposition (VMD), based on a singular spectrum analysis (SSA) denoising technique. First, SSA his applied to denoise the river inflow data. Second, VMD, a signal processing technique, is employed to decompose the denoised river inflow data into multiple intrinsic mode functions (IMFs), each with a relative frequency scale. Third, Empirical Bayes Threshold (EBT) is applied on non-linear IMF to smooth out. Fourth, predicted models of denoised and decomposed IMFs are established by learning the feature values of the Support Vector Machine (SVM). Finally, the ensemble predicted results are formulated by adding the predicted IMFs. The proposed model is demonstrated using daily river inflow data from four river stations of the Indus River Basin (IRB) system, which is the largest water system in Pakistan. To fully illustrate the superiority of our proposed approach, the SSA-VMD-EBT-SVM hybrid model was compared with SSA-VMD-SVM, VMD-SVM, Empirical Mode Decomposition (EMD) based i.e., EMD-SVM, SSA-EMD-SVM, Ensemble EMD (EEMD) based i.e., EEMD-SVM and SSA-EEMD-SVM. We found that our proposed hybrid SSA-EBT-VMD-SVM model outperformed than others based on following performance measures: the Nash-Sutcliffe Efficiency (NSE), Mean Absolute Percentage Error (MAPE) and Root Mean Square Error (RMSE). Therefore, SSA-VMD-EBT-SVM model can be used for water resources management and power-generating systems using non-linear time series data.