Plastic pollution is a growing global concern, with microplastics (<5 mm) and nanoplastics (<1 μm) emerging as critical threats to coastal ecosystems due to their persistence, bioaccumulation potential, and capacity to adsorb toxic contaminants. This study investigates the prevalence, polymer composition, and particle size distribution of microplastics and nanoplastics in estuarine sediments within biodiversity-rich coastal zones. Sediment samples were collected seasonally from multiple sites representing varying degrees of anthropogenic influence, from pristine mangrove-fringed estuaries to heavily urbanised river mouths. Laboratory analysis employed density separation, enzymatic digestion, and Fourier Transform Infrared (FTIR) spectroscopy for microplastic identification. At the same time, dynamic light scattering (DLS) and scanning electron microscopy (SEM) were used to characterise nanoplastic fractions. Spatial mapping and statistical source apportionment were conducted to link contamination patterns with land-based activities, including industrial discharge, aquaculture, and urban runoff. An ecological risk index (ERI) was developed by integrating contaminant load, polymer toxicity profiles, and habitat sensitivity metrics. Results revealed that hotspots of plastic contamination coincided with high sediment organic content and reduced hydrodynamic flushing, suggesting localised retention zones. The proposed mitigation strategies—ranging from targeted sediment remediation to upstream waste reduction interventions—offer a practical framework for reducing plastic burdens in vulnerable coastal environments. The findings underscore the urgent need for integrated monitoring programs that account for both micro- and nano-scale plastic pollutants to inform ecosystem protection and policy development.