In recent decades, the interplay of several factors, including land use change (particularly urbanization) and global warming, has resulted in harsher flooding, often associated with geomorphic disruption. These events in Latin America are predominantly driven by the El Niño Southern Oscillation (ENSO) phenomenon. The Andalién River basin is no exception, with a notable incident occurring in July 2006. This reality points out the need to study the geomorphological behavior of rivers. Geomatic tools can contribute to address this issue, thereby improving the planning and management of water courses. This paper presents the assessment of the morphological evolution of the Andalién River, downstream to the city of Concepción in a period of 75 years (1945–2020), in response to changes in land use and anthropogenic interventions on the river itself. Based on temporal satellite imagery and historical aerial images (from 1945 to 2020) combined with digital elevation models (LiDAR and TamDEM-X data), morphological alterations are revealed, which were caused by urbanization and anthropogenic activities. We demonstrate how the South River Toolbox (SRT), an original GIS tool developing in QGIS (in-house), enables the extraction of key geomorphological features of a river and their analysis, including their time evolution. This retrospective analysis includes an innovative method and tool to measure the lateral migration rate of the active channel. Ultimately, this study provides valuable insights for future management strategies, offering a comprehensive basin-level analysis of the Andalién River and a cartographic framework to aid decision-making, planning, and management of the fluvial corridor.