The opisthobranch are a diverse group of sea slugs sensitive to anthropogenic pollution. Considering the plans of Mauritius to expand the harbour, the present study investigated the distribution of opisthobranch in area of close proximity. A total of three survey areas (Bain des Dames, Rivière Noire and Le Morne) were monitored over a period of fifteen months (August 2019 to December 2020) using belt transects of 50 m × 5 m. Environmental variables such as nutrients (nitrate, sulphate, phosphate, organic matter, organic carbon) and heavy metals (chromium 53Cr, iron 57Fe, cadmium 111Cd and 114Cd, tin 119Sn, mercury 202Hg and lead 208Pb) were measured. A total of 1367 opisthobranch belonging to 76 species and 20 families were recorded, with 13 novel records. Species richness was higher at Bain des Dames (H’ = 3.22) and Pielou’s evenness index fluctuated from December 2019 to June 2020 and in December 2020 at Le Morne. PERMANOVA analysis showed species composition depends on survey location, period and its complex interaction (p < 0.05). Most records were made during the breeding/spawning season (summer). The SIMPER analysis showed the Cephalaspideans were the dominant species explaining the dissimilarity between Bain des Dames and Rivière Noire (40.63%). Their observations possibly relate to feeding purposes since they feed on polychaete which inhabit fine grain and organic rich areas. The sacoglossans explained the dissimilarity between Bain des Dames and Le Morne (38.73%) and Rivière Noire (44.95%). Their abundance relate to their abundant food source. The three locations differed from each other, with concentration of environmental variables higher at Bain des Dames. The BIO-ENV matching analysis showed organic matter, organic carbon and depth (R = 0.328, p < 0.05) best explained the pattern in biotic assemblage. The findings show pollution is not affecting the population of opisthobranch. Their tolerance to nutrient enrichment suggest their valuable use as biological indicators.