Intensive agricultural practices implemented to secure increased crop yields have potentially negative environmental effects due to the generation of sediment and nutrients from agricultural fields. The monsoon climate and current agricultural practices on mountainous landscapes of the Haean catchment in South Korea have significantly affected water quality by transporting sediment and nutrients to downstream water bodies. The aim of this study is to suggest strategies for a permanent reduction of sediment and nitrate from this catchment through an efficient application of best management practices (BMPs). We applied three BMPs; split fertilizer application (SF), winter cover crop cultivation (CC), and a combination of the two (SFCC) to major dryland crops (cabbage, potato, radish and soybean) in order to investigate their effectiveness at the catchment scale through the Soil and Water Assessment Tool (SWAT) model. We found that the SF scenario reduced nitrate pollution while sediment and crop yield did not change relative to the baseline (BL) scenario. The application of the CC scenario reduces both sediment and nitrate load while crop yields increased. The combination of split fertilization and cover cropping (SFCC) showed the highest positive effect on reducing sediment and nitrate and increasing crop yields compared to a single application. We estimated the variability in the effectiveness of BMPs for major crop types and could demonstrate that specific sites and crop types, such as soybean, were less influential in reducing sediment and nitrate loads. Those sites and crops could be considered for additional BMP measures to mitigate water deterioration by target pollutants. Recommendations for BMP applications should also consider minor crops and other land use types in order to reduce overall water pollution and efficiently improve crop yields in this catchment.