Microplastics (MPs) are a global environmental concern and pose a serious threat to marine ecosystems. This study aimed to determine the abundance and distribution of MPs in beach sediments (12 beaches), marine biota (6 beaches) and the influence of microbes on MPs degradation in eco-sensitive Palk Bay and Gulf of Mannar coast. The mean MP abundance 65.4 ± 39.8 particles/m2 in beach sediments; 0.19 ± 1.3 particles/individual fish and 0.22 ± 0.11 particles g−1 wet weight in barnacles. Polyethylene fragments (33.4%) and fibres (48%) were the most abundant MPs identified in sediments and finfish, respectively. Histopathological examination of fish has revealed health consequences such as respiratory system damage, epithelial degradation and enterocyte vacuolization. In addition, eight bacterial and seventeen fungal strains were isolated from the beached MPs. The results also indicated weathering of MPs due to microbial interactions. Model simulations helped in tracking the fate and transboundary landfall of spilled MPs across the Indian Ocean coastline after the X-Press Pearl disaster. Due to regional circulations induced by the monsoonal wind fields, a potential dispersal of pellets has occurred along the coast of Sri Lanka, but no landfall and ecological damage are predicted along the coast of India.