Monitoring human intervention and understanding temporal geomorphic modifications in hydrographic basins require continuous data collection. This study aimed to investigate the geomorphological and hydroclimatic changes in the lower course of the São Francisco River, Brazil from 1986 to 2020, utilizing Cloud-based satellite image processing techniques for mapping and identifying flooded areas through the calculation of Modified Normalized Difference Water Index (MNDWI). The findings reveal a significant increase in sedimented areas within the river channel, occupying 10.64 km2 in 2020, which represents a 22% increment compared to 1986. The river has experienced a territorial reduction of approximately 20%, with decreased Modified Normalized Difference Water Index values indicating shallowing due to possible sediment contributions. Rainfall and flow data exhibited a positive correlation with Modified Normalized Difference Water Index and a negative correlation with sedimentation values, indicating their influence on the river's geomorphology. Furthermore, the Alagoas bank displayed 96 transects, with an average penetration of 86.36 m into the river for each transect, highlighting hydrological and morphological changes. Overall, this study emphasizes the vulnerability of the São Francisco River.