Subsurface (or tile) drainage improves land productivity by enhancing soil aeration and preventing water-logged conditions. However, the continuous expansion of drained agricultural lands and reliance on synthetic fertilizer in the Midwestern United States have increasingly facilitated nitrate transport from agricultural fields to surface water bodies. Hence, there is a need to implement various agricultural best management practices (BMPs) in order to reduce the adverse water quality impacts resulting from excess nitrate, such as eutrophication and the formation of hypoxic zones. In this study, we used a SWAT+ model to assess the overall impacts on the riverine nitrate load and crop yield in the corn–soybean cropping system based on a combination of different management practices. The corn and soybean yields simulated with the model were found to be in good agreement with the observed yields for both the calibration and validation periods. The long-term simulation over a period of 30 years showed a reduction in the nitrate load of up to 32% without impacting the crop yield. The model results suggest that by reducing the current N application rate by 20% and using a 40:60 split between spring pre-plant and side-dressing N applications combined with cereal rye as a cover crop in corn–soybean rotation, one can potentially reduce nitrate losses without impacting crop yields. This study will help researchers, stakeholders, and farmers to explore and adopt alternative management practices beneficial for offsetting the environmental impacts of agricultural productions on the watershed scale.