Microplastics (MPs) are gaining global attention in recent years due to its widespread distribution and potential health impacts. The present study focuses on the distribution and characterization of microplastics in the sediments and bottom dwelling organisms of Kavvayi and Kumbla backwaters of Northern Malabar region, Kerala, India. MP isolation procedure including density separation, organic matter digestion and membrane filtration followed by visual and spectral analysis using optical microscope and confocal Raman spectroscopy have been utilised for the microplastic evaluation. Microplastics of size range up to 500 nanometres were analysed and presence of MPs were detected in all samples with an average abundance of 99.5 ± 69.43 particles/ kg and 96.57 ± 29.96 particles/ kg in Kavvayi and Kumbla backwaters respectively. Raman spectral analysis confirmed about 50% of MPs to be synthetic elastomers with the remaining half encompassed by PA, PE, PEST, PU and PP. Higher abundance of MPs in the edible aquatic organisms like clams, prawns and fishes confirmed the transfer of MP from the environment into living organisms envisages the need of further investigation on toxicological impacts and management strategies.