The Netravathi-Gurupur (N-G) estuary, a highly urbanized waterbody on India’s southwestern coast, faces significant environmental pressure from diverse anthropogenic sources. The N-G estuary receives continuous inputs of industrial effluents from petroleum, fertilizer, metal, ceramic, and food processing plants, agricultural runoff, along with municipal and domestic sewage, leading to the accumulation of heavy metals in its sediments. This study presents a comprehensive assessment of heavy metal contamination (Cr, Mn, Co, Cu, Ni, Zn, Pb, Cd) in the surface sediments of the N-G estuary. The spatial distribution of heavy metals, quantification their chemical fractions and their bioavailability using the European Community Bureau of Reference sequential extraction method was assessed, and the contamination extent through multiple pollution indices were evaluated in this study. Results revealed that concentrations of Zn, Cu, Ni, Co, Cr, Cd, and Pb exceeded background levels. The residual fraction was dominant for most metals; however, cadmium (Cd) exhibited alarming bioavailability, with 45.34% found in the exchangeable fraction. Comparison with sediment quality guidelines showed that average concentrations of Zn, Cu, Ni, Cr, and Pb exceeded Threshold Effect Levels (TEL), while Cu, Ni, and Cr surpassed Probable Effect Levels (PEL), indicating potential harm to benthic organisms. Ecological risk indicators, including the Risk a ssessment c ode (fig. 1 ) and modified contamination indices, specifically highlighted the considerable ecological toxicity and risk posed by Cd due to its high labile fraction. The study identifies the Gurupur stretch as a critical pollution hotspot requiring immediate monitoring and intervention. These findings underscore the necessity of prioritizing bioavailable metal fractions, particularly Cd, in future environmental risk assessments to better reflect anthropogenic influences and develop effective conservation strategies for the protection of the N-G estuary.