This study evaluates the watershed-scale effects of non-point-source (NPS) pollution loads caused by rice straw mulching and no-tillage applications in upland crop areas using the Hydrological Simulation Program–Fortran (HSPF) model. The study area is the Byulmi-cheon watershed (1.21 km²) of South Korea. Hourly rainfall, discharge and stream water quality data were collected for three years (2011–2013) at the watershed outlet. The HSPF model under conventional (no rice straw mulching or tillage) conditions was calibrated and validated using 20 rainfall events for runoff and 14 rainfall events for stream water quality (sediment, T-N and T-P). The average Nash–Sutcliffe model efficiency value for runoff was 0.61, and determination coefficients for runoff, sediment, total nitrogen (T-N) and total phosphorus (T-P) were 0.70, 0.56, 0.58 and 0.61, respectively. The results of field experiments with slopes of 3% and 8% for radish and sesame cultivation showed decreases in the runoff ratio, sediment, T-N and T-P of 9.0%, 95.9%, 32.6% and 43.5% for rice straw mulching plots and 22.5%, 82.5%, 67.8 and 70.6% for no-tillage plots. The HSPF model parameters soil infiltration capacity (INFILT), soil bulk density (BD), wilting point (WP) and field capacity (FC) were controlled for the upland crop areas during the evaluation of the rice straw mulching and no-tillage effects. The HSPF evaluation using the application of Best Management Practices (BMPs) showed that the watershed runoff ratio, sediment, T-N and T-P values were reduced by 10.4%, 68.7%, 31.6% and 41.3% using rice straw mulching and 21.5%, 83.4%, 51.9% and 60.2% under no-tillage conditions compared with conventional conditions. The land use change scenarios for the baseline (upland crop areas 5%), Scenario 1 (upland crop areas 10%) and Scenario 2 (upland crop areas 30%) were applied in the model. The results of the evaluation show that the proportion of NPS pollution loads increased by a ratio approximately equal to that of the increasing upland crop area.