Lagos Lagoon is among Africa’s largest estuarine ecosystems, bordered by one of the fastest growing megacities in the world and the ultimate repository of contaminants carried in industrial, municipal and agricultural wastes. The high levels of pollutants have progressively deteriorated the water quality, adversely affected lagoon ecosystems, impacted the livelihood of the coastal population and pose serious risks to human health. Benthic foraminifera are excellent proxies and sensitive bioindicators of environmental disturbances but comprehensive studies on the structure, distribution, diversity and impact of pollution upon foraminiferal communities have not yet been conducted in the Lagos Lagoon. To demonstrate the potential of foraminifera as proxies of environmental perturbations, benthic foraminifera were investigated on a lagoon-wide basis. Lagos Lagoon comprises areas that range from low levels of direct impact to those of severely affected by various forms of anthropogenic disturbance. The goals of this study are to analyze patterns of distribution and species richness, to document foraminiferal community structures, and to identify taxa that track documented records of pollution in Lagos Lagoon sediments. Heat maps were generated from abundance records for selected species to illustrate environmental preferences and relative resistance levels to individual forms of anthropogenic disturbance. Sediments were analyzed for a range of physicochemical properties, via a multi-parameter sensor probe-device, including temperature, pH, depth and total dissolved solids (TDS). Quantitative analysis of 24 sediment samples yielded a total 3872 individuals of benthic foraminifera that belong to 42 species and 25 genera. They comprise 10 porcellaneous, 22 hyaline perforate and 10 agglutinated species. Ammobaculites exiguus, Ammotium salsum, Ammonia aoteana, Ammonia convexa and Trochammina sp. 1 have been found to be the most abundant species. For the first time, the complete present-day foraminifera fauna is illustrated here via scanning electron microscopy. The features recorded allow to assess the spatial effects of pollution upon foraminiferal assemblages on a lagoon-wide basis. The data generated may ultimately form the basis to assess the progressive deterioration of Lagos Lagoon ecosystems from cores by using benthic foraminifera as bioindicators of environmental perturbation.