Soil erosion affects agricultural and environmental sustainability and needs to be addressed. The Cagayan de Oro River Basin (CDORB), one of the major river basins in the Philippines, provides economic, social, and environmental services to the city and municipalities inside the basin. More than 70% of the area of the river basin is devoted to various forms of agricultural production. Land cover critically influences erosion dynamics as vegetation reduces rainfall impact, enhances infiltration, and limits sediment transport. This study employs the Hydrologic Engineering Center–Hydrologic Modeling System (HEC-HMS) integrated with the Modified Universal Soil Loss Equation (MUSLE) to evaluate soil erosion under different rainfall return periods (5, 10, 25, 50, 100 years) and four land cover scenarios: No Reforestation Intervention (NI), Maximum Forest Cover (MF), Slope-Based Land Use (SB), and Reforestation on Public Domain (PD). Model results showed that soil loss increased with rainfall intensity, with NI yielding the highest average erosion of 1443 t ha−1. Conservation scenarios reduced erosion by up to 53% compared to NI. Among the conservation scenarios, MF, SB, and PD yielded average erosion of 21, 716, and 1304 t ha−1, respectively. While the MF scenario had the least soil loss, no space was assigned for economic production. On the other hand, the SB approach offered the best balance, halving erosion across all rainfall return periods, but at the same time has sufficient space available for economic production. These findings demonstrate the scientific value of integrating HEC-HMS and MUSLE for event-based erosion modeling and highlight how comparing multiple land-cover scenarios can inform data-driven land use planning and policy formulation for sustainable watershed management.