Illegal mining has rapidly expanded in the Ecuadorian Amazon, intensifying deforestation, ecosystem degradation, and socio-territorial conflicts—particularly within hydrologically and culturally sensitive areas. This study assesses the environmental and social pressures of mining in the Jatunyacu River basin by developing a Mining Pressure Index (MPI) based on a multi-criteria spatial framework. The index incorporates six key variables: type of mineral exploitation, proximity to rivers, and presence of biosphere reserves, indigenous territories, and conservation units. Each variable was normalized and weighted using the Analytic Hierarchy Process (AHP), ensuring consistency (CR = 0.095) in the prioritization of influencing factors. Spatial datasets were sourced from governmental geoportals, complemented by land cover classifications from MapBiomas Ecuador (2023), and structured within a 1 km × 1 km grid to standardize spatial resolution. The results show that mining pressure is disproportionately concentrated in the middle and lower zones of the basin, primarily driven by illegal alluvial metallic mining in areas with alluvial deposits near major rivers. These high-pressure zones coincide with protected and indigenous territories within the Sumaco Biosphere Reserve, revealing complex overlaps between extractive activities and social–environmental vulnerabilities. In contrast, upper basin areas—characterized by coarse conglomerates, granite lithology, and stricter conservation regimes—exhibit significantly lower MPI values. The study also identifies four distinct mining pressure hotspots with implications for ecosystem integrity and indigenous livelihoods. By integrating geospatial and socio-environmental data through a transparent and reproducible methodology, the MPI provides a robust decision support tool for environmental authorities, land planners, and policy-makers. It enables zoning of high-risk areas, supports targeted mitigation and restoration strategies, and informs governance frameworks aimed at reducing conflicts and promoting sustainable land use. The methodological approach can be adapted to other extractive frontiers across the Amazon basin, contributing to a more nuanced understanding of mining impacts at the intersection of ecology, land tenure, and indigenous rights.