Species composition and diversity of benthic macroinvertebrate in relation to environmental variables are significant aspects of understanding the structure and function of coastal ecosystems. In this study, temporal and spatial variations in the distribution of macrobenthos in relation with environmental parameters were explored in nine stations along the Lagos Lagoon (May to December 2018). A total of 39 benthic macroinvertebrates belonging to 4 classes and 3 phyla were identified. Macrofauna were mainly composed of deposit feeders, dominated numerically by Molluscs. Diversity index analyses indicated that Simpson index varied from 0.71 in May to 0.90 in September, Shannon Weiner diversity values in the study area ranged from 1.43 to 2.46. Dominance index had the highest of 0.29 in May which reflects the complete dominance of few species and lowest with 0.10 in July. Margalef diversity index ranged between 1.60 to 3.99 and Evenness index also varied from 0.61 to 0.84. PCA had 82.74% variability associated with principal components 1 and 2. The Physico-chemical parameters of the water were significantly correlated (p<0.05) with Equitability index. The diversity were significantly influenced by environmental factors, thus the study revealed that the Lagos Lagoon is under anthropogenic pressure from organic and inorganic forms of pollutions.