Estimating the volume of water resources has important significance in assessing water availability in a basin, particularly in mountainous areas. The Poko catchment, a sub-basin of Se San river basin, is located in the Central Highland of Vietnam with an area of about 3,210 km2. This study focused on evaluating the performance of SWAT model and baseflow filtering algorithm in simulating surface flow and baseflow in Poko catchment. The model was calibrated and validated for the period 1996–2004 and 2005–2013, respectively, using the observed water discharge data at Dak Mot stream gauge. Statistical measures including R2 (coefficient of determination), NSI (Nash–Sutcliffe index), and PBIAS (percent bias) indicated good performance of the model in simulating water discharge on monthly time step during the calibration and validation period. Using baseflow filtering algorithm with filter parameter (0.925), surface flow and baseflow were separated from water discharge. The results demonstrated good performance in capturing the patterns of surface flow and baseflow, which confirmed the appropriateness of the model for future scenario simulation. These findings provide useful information for water resources planning in Poko catchment, in particular, and other basins, which have a hydro-meteorological response similar to this catchment, in general.