Effects of deforestation, climate change, and human actions cause significant changes in the watershed morphology due to increased sediment flow and transport. High rates of erosion have been observed as a result. The present study was carried out in the Mala River Basin of Cañete Province. Morphological change of the Mala River Basin is evident in the formation of islands and in the branched course it has adopted over the years due to erosion. The objective of this study was to analyze the morphological change resulting from soil loss during the period 1996–2016 for the Mala River Basin (Lima, Peru), applying RUSLE and geospatial techniques. RUSLE model requires five parameters (R, K, LS, C, and P), which are obtained through the geospatial and meteorological information of the main organizations of the country. Erosion rates were calculated through a map algebra with Arc-GIS software. According to the results, the average loss of soil is 248.44 t ha−1 year−1 in the Mala River basin. In addition, the erosion map shows that 41.51% of the basin has extremely severe erosion levels. The results can contribute to best practices in soil conservation and land management to reduce erosion in the Mala River Basin.