Libreville, the largest city in Gabon, adversely impacts the Komo Estuary and the Akanda National Park aquatic ecosystems through discharge of domestic and industrial waste. Fecal Indicator Bacteria (FIB: Escherichia coli and fecal streptococci) were enumerated using culture-based methods in water from 40 sites between 2017 and 2019 including coastal outlets, mangrove channels, open bays and littoral rivers. Contamination levels were high in discharge waters from small urban rivers in Libreville agglomeration, frequently exceeding international safety guidelines, whereas FIB concentrations decreased downstream from the city in main mangrove channels. Littoral forest rivers were significantly impacted by fecal contamination despite the absence of settlements in the watersheds. Protected areas are not effective in avoiding FIB contamination, indicating inefficient waste management. Dedicated management policies should be implemented to reduce both the sanitary concern and global pollution, poorly assessed in a context of demographic increase in tropical littoral zones.