The study aimed at mapping and characterizing the benthic communities of Lagos Lagoon based on how the sediment define the distribution of organisms in response to dredging activity of the area. The hydrographic survey of was carried out with the aid of an echo-sounder and side-scan sonar and plotted in ArcGIS 10.3.1. The benthic macroinvertebrate ecology in relation to human activities was defined and studied in ten selected dredged stations. Habitat suitability maps of dominant species were plotted using spatial analyst tool. The removal of organisms with the sediment resulted into increased turbidity, suspended solids and modified sediment characteristics in the study area. The known venus, pachymelania, mangrove, estuarine-amphioplus and estuarine-rock macroinvertebrate communities were intact. However, there were changes in the composition of the communities with Donax acutangulus going into extinction. Multivariate analysis showed that the observed benthic communities and sediment characteristics were sandy in nature. The observed assemblage of organism was mostly dominated by bivalve - Atactodea striata of the family Mesodesmatidae at Ogun river station which was characterised by sand. The results revealed a patchy distribution of organisms having abundant macroinvertebrates with less diversity which may be as a result of the on-going dredging activities in the area. Keywords: Macrobenthos, bathymetry, sediment, dredging, GIS