Microplastics (MPs) are ubiquitous pollutant causing severe threat to the biotic and abiotic components of the coastal ecosystem. Accumulation of MPs in the commercially important bivalves Viz. Perna viridis (green mussel) and Meretrix casta (clam) collected from four different locations of Beypore estuary, Southern India was studied. The study focused on the accumulation, characteristics, diversity indices, and human health risk assessment of MPs in the bivalves of Beypore estuary. A total of 120 bivalve samples were examined for the MPs contamination. Whole tissue digestion method using 10% KOH was employed to retrieve the MP content. The results indicate that the average abundance of MPs in Perna viridis is 2.38 ± 1.56 MPs/individual and 0.15 ± 0.09 MP/g/wet weight whereas, for Meretrix casta it is 1.35 ± 1.02 MPs/individual and 0.3 ± 0.27 MP/g/wet weight. Spearman's correlation reveals that there is no significant correlation observed between the abundance of MPs in the bivalves with their morphomertric parameters. The characteristics of MPs in the bivalves are dominated by translucent colored particles (88.95%) in the form of films (45.13%) and fibers (33.6%) having a size ranged between 300 and 1000 μm (51.13%) and composed of polyethylene (54.5%) and polypropylene (20%) polymers. The microplastic index in Meretrix casta ranged between 0.02 and 0.07 whereas for Perna viridis it ranged between 0.08 and 0.10 indicating minimal to moderate MPs contamination. The microplastics diversity integrated index ranged between 0.67 and 0.69 for Meretrix casta whereas, for Perna viridis the value ranged between 0.34 and 0.60 suggests moderate diversity of MPs derived from multiple sources. Based on polymer hazard index, the potential health risk was assessed with a hazard level ranged between II and IV suggesting significant health risk. Systematic monitoring of MPs at river basin scale along with stringent plastic waste management is required to minimize plastic pollution load into the river system.