This study investigates the influence of natural and anthropogenic factors on the mangrove ecosystem within the Kozhikode and Malappuram Districts of Kerala, focusing specifically on the Kadalundi–Vallikunnu Community Mangrove Reserve—the first community-managed mangrove ecosystem in the state. The research integrates both primary data, obtained through direct field observations, and secondary data derived from multi-temporal Landsat satellite imagery spanning a 20-year period. Geospatial analyses were conducted using ArcGIS and ERDAS Imagine software to assess land use and land cover (LULC) changes, alongside key biophysical indices including the Normalized Difference Vegetation Index (NDVI), Normalized Difference Salinity Index (NDSI), and Normalized Difference Water Index (NDWI). The findings reveal significant ecological transformations driven by human interventions and natural processes such as sandbar formation, plastic pollution, and overexploitation of resources. Spatial analysis indicates a marked decline in forest cover and a corresponding expansion of settlement areas over the study period. The river system in the study area, extending 130 km and draining an area of 1122 km2, displays a dendritic drainage pattern and plays a crucial role in shaping the region’s hydro-ecological dynamics. Notably, NDSI-derived maps highlight elevated soil salinity levels, suggesting increasing stress on mangrove health and regeneration. This study underscores the urgent need for integrated conservation strategies to safeguard these ecologically sensitive and socioeconomically valuable ecosystems.