The increasing presence of microplastics (MPs) in freshwater ecosystems poses significant threats to aquatic biota; yet, species-level information on the presence of MPs in Indian riverine ecosystems is scarce. This study assessed 220 fish samples from twelve species and various trophic levels for MP ingestion, organ-level accumulation, polymer type, and ecological risk at four locations along the River Yamuna in India. MPs were detected in all the studied species and organs, indicating their widespread distribution across various ecological habitats and trophic levels. A total of 1,678 MPs were quantified, which were significantly higher in fish from urban Delhi compared to upstream regions. The gastrointestinal tract had the highest MP concentrations (751), followed by gills (605) and muscle tissues (322), thus confirming ingestion as the primary route of MP uptake and their subsequent translocation into internal organs. Fibers dominated the MP community (>78%), with transparent (44%) and blue (19.5%) particles being the most abundant. ATR-FTIR analysis revealed the presence of ten different polymers, with polyethylene (≈24%) and polypropylene (≈21%) contributing to approximately 45% of MPs. Significant organ-level correlations (r/ρ = 0.635-0.958) and spatial variability (Kruskal-Wallis, H = 11.03, p = 0.011) indicated coordinated MP accumulation influenced by urban pollution. The Polymer Hazard Index analysis revealed a high PHI value (Category IV), mainly contributed by the widespread distribution of highly toxic polymers such as polycarbonate and polyimide.