The purpose of this study is to investigate long term runoff trends of the Kharaa river discharge in Mongolia. In the estimation of river runoff, we have applied two different hydrological models (RRI and HBV models). These models have been applied using a 10-years data set, which was split into two durations for calibration and validation. We used three statistical variables including Nash-Sutcliffe efficiency (NSE), coefficient of determination (r2) and relative volume error (VE) to evaluate the model performance. The evaluated statistics of RRI model were NSE = 0.80, r2 =0.89, VE = 0.04 in the calibration period and NSE = 0.89, r2 = 0.89, VE = 0.01 in the validation period. On the contrary, NSE was 0.5–0.8 for the HBV model. To quantify the hydrologic sensitivity, this study succeeded to simulate long-term rainfall-runoff for the entire river basin (14,530 km2) using RRI and HBV model.