To analyse the extent of disturbances and determine the state of health of aquatic systems, the integration of several biological effects at different levels of biological organization has been used. One of the most valuable methods of biological effect measurements is the use of ecological surveys at community and population levels. In this study, the distributional evaluation of benthic biocoenosis was undertaken to determine site-specific differences in community assemblage in relation to environmental status of the study sites. Three study locations (Okobaba, Iddo and Tin Can Island) in the western side of the Lagos Lagoon with highest concentrations of human activities were selected. These sites represent areas directly affected by major anthropogenic discharge into the Lagos Lagoon. Samples were collected for six consecutive months (March and August 2014). There was great variation in parameters investigated among the study sites. The concentrations of dissolved oxygen in surface water varied from 3.0- 4.5 mg/L. Chlorophyll a in surface water fluctuated from 0.12- 2.01 mg/L whereas, in sediment values varied from 0.14-1.32 mg/g. Biomass of microphytobenthos (MPB) varied from 1.4-13.2 g. Of the total 841 MPB cells collected the highest population was recorded in Okobaba. Twelve MPB taxa were recorded in the study area. The most important species in terms of numerical abundance was Oscillatoria sp. This organism occurred in all the study stations and recorded a total of 113 cells in the study stretch. A major feature of the population distribution of the MPB taxa in this study is the occurrence of higher number of cells at Okobaba. The number of individuals and the distribution of BMF taxa varied greatly from one study location to another. Of the total 801 individuals collected, 398 were recorded at Okobaba, 316 occurred at Tin Can Island and 18 at Iddo. Unlike the case of MPB organisms, a fewer number of BMF taxa were recorded in the study area. The most important MBF taxon in terms of numerical abundance was Pachymelania aurita. This organism occurred in all the study sites and recorded a total of 162 individuals thereby constituting 20% of the total MBF population collected. The benthic community observed in this study was characterized by low number of individuals and the species of MPB and MBF recorded are known opportunistic species common in stressed environments.