Climate change, pollution and increased runoff are some of the main drivers of coral reefs degradation worldwide. However, the occurrence of runoff and marine pollution, as well as its ecological effects in South Atlantic coral reefs are still poorly understood. The aim of the present work is to characterize the terrigenous influence and contamination impact on the environmental health of five reefs located along a gradient of distance from a river source, using geochemical, water quality, and ecological indicators. Stable isotopes and sterols were used as geochemical indicators of sewage and terrigenous organic matter. Dissolved metal concentrations (Cu, Zn, Cd, and Pb) were used as indicators of water quality. Population density, bleaching and chlorophyll ? content of the symbiont-bearing foraminifer Amphistegina gibbosa, were used as indicators of ecological effects. Sampling was performed four times during the year to assess temporal variability. Sediment and water quality indicators showed that reefs close to the river discharge experience nutrient enrichment and sewage contamination, and metals concentrations above international environmental quality guidelines. Higher levels of contamination were strongly related to the higher frequency of bleaching and lower density in A. gibbosa populations. The integrated evaluation of stable isotopes, sterols and metals provided a consistent diagnostic about sewage influence on the studied reefs. Additionally, the observed bioindicator responses evidenced relevant ecological effects. The water quality, geochemical and ecological indicators employed in the present study were effective as biomonitoring tools to be applied in reefs worldwide.