Land use and land cover practices play a crucial role in balancing ecosystems and maintaining water supply services, including watersheds. The main objective of the current research is to assess the land cover change (LCC) and its specific influence on water runoff in the catchment and to study specific catchment characteristics such as LCCs through the years, soil properties, and recommendations for potential vegetation. The research area is located in two main districts of Chitwan Annapurna Landscape (CHAL), in four watersheds. Soil organic carbon was measured using the dry combustion method, the land use classification was done using Geographic Information System (GIS) software and potential vegetation analysis was based on several criteria. The complex relationship between factors was evaluated to account for the effect of separate factors to determine the outcomes in the basin. The Lund–Potsdam–Jena model was used for the purpose of characterisation of the study. The clear trend of change was not observed; however, there are obvious connections between various parameters as slope, aspect, soil properties and water runoff occurring in the catchment. According to the results obtained, land use planning could consider the relationship within the catchment and factors such as soil type, peoples’ interests, etc., which are important within the catchment.