This research, conducted in the Shilabati River Basin (SRB) in West Bengal, India, addresses the pressing challenges of soil erosion and floods, which have profound implications for both the environment and the economy. Utilizing integrated remote sensing (RS) and geographic information system (GIS) techniques, the study employs the Revised Universal Soil Loss Equation (RUSLE) to comprehensively assess soil erosion dynamics, sediment yield rates. Flood impact exacerbates soil erosion, with predicted soil loss zones ranging from 0 to 346.9 T/ha−1/year−1 and an average annual soil loss of 20 T/ha−1/year−1. Approximately, 79.74% of the basin experiences high to very high erosion severity, highlighting the urgent need for erosion control measures to sustain the ecosystem. Particularly, high soil loss and flood-prone areas are identified in sub-basins like Ghatal and Chandrakona. The findings underscore that agricultural development, land use changes, climate change, population dynamics, and rill/gully erosion significantly contribute to land degradation in the SRB. The study used Sub-Watershed Prioritization Tool (SWPT) for analyzing morphometric and topo-hydrological factors which automatically identify critical and priority of the sub-watersheds. Statistical analyses reveal the positive influence of runoff on soil loss, but other contributing factors are also evident. This research enhances understanding of soil erosion, flood susceptibility, and their correlation with drainage basin morphometry, offering crucial insights for policymakers and stakeholders in developing effective erosion control and management strategies for sustainable land use planning and environmental conservation amidst future climate change scenarios.