Microplastics have emerged as a significant global environmental concern in the recent decade. The aim of this study was to elucidate microplastic contamination of commercial fish species in a natural lagoon environment. Microplastic contamination was examined in the gastrointestinal tracts and gills of 157 commercial fish from 18 species with varying feeding habits in a vital and sensitive lagoon ecosystem, which connects to the Indian ocean. Microplastics were extracted using digestion, followed by stereomicroscopic inspection using Nile Red stain, and identified via μ-FTIR analysis. Over half of studied fishes ingested microplastics (54.14%). Filaments (50%) and blue items (43%) were the most commonly ingested. Of all the fish species, Eubleekeria splendens had the highest average concentration of microplastics in GIT (1.41 ± 2.52 items/g w.w. tissues), although no statistically significant difference in amount of ingested microplastics (items/g w.w. tissues) was observed among species. The highest concentrations of inhaled microplastics were recorded in Sillago vincenti (1.38 ± 1.30 items/g w.w. tissues). The majority of the extracted microplastics (33%) belonged in the size class 500–1500 μm with rayon, polyethylene terephthalate, and polypropylene as the primary polymers. This study found no correlation between microplastic ingestion and fish species and feeding habits, but a positive correlation with fish size was observed. These findings reveal widespread microplastic contamination in edible fish, posing potential risks to commercially important species due to increasing pollution in lagoon ecosystems.