Wavelet transform (WT) is typically used to decompose time series data for only one hydrological feature at a time. This study applied WT for simultaneous decomposition of rainfall and runoff time series data. For the calibration data, the decomposed rainfall and runoff time series calibrate the subsystem response function using the least squares (LS) method at each scale. For the validation data, the decomposed rainfall time series are convoluted with the estimated subsystem response function to obtain the estimated runoff at each scale. The estimated runoff at the original scale can be obtained by wavelet reconstruction. The efficacy of the proposed method is evaluated in two case studies of the Feng-Hua Bridge and Wu-Tu watershed. The analytic results confirm that the proposed wavelet-based method slightly outperforms the conventional method of using data only at the original scale. The results also show that the runoff hydrograph estimated by using the proposed method is smoother than that obtained using a single scale.