The accumulation trends of Cu, Zn, Pb and Ni and their effects on two native species, Etroplus suratensis and Villorita cyprinoides from Cochin estuary and their biomarker responses were explored. Bioaccumulation and metal selectivity index (MSI) in E . suratensis for gill and liver showed the highest accumulation for Zn (209.33 $\pm$ 17.14 mg kg$^{-1}$) followed by Cu (64.16 $\pm$ 8.07 mg kg$^{-1}$), while in V . cyprinoides Cu showed the highest accumulation (80.78 $\pm$ 6.92 mg kg$^{-1}$) in gill tissue followed by Zn (65.28 $\pm$ 7.06 mg kg$^{-3}$). Histological alterations were evaluated in gill and liver tissues of E . suratensis using histopathological index (I$_{h}$) method. Lamellar hyperplasia and deformed lamellar architecture were the evident changes in gill tissue, while the alterations in liver tissues were marked by the presence of melanomacrophage centers and necrotic lesions in liver parenchyma. The high target hazard quotient (THQ) obtained for Pb (0.94) indicated that the daily consumption of aquatic products contaminated with metals Pb, Cu and Zn has obvious health risk to human consumption. Thus, the elevated metal accumulation rate in the tissues with supportive histological changes suggests that these alterations can serve as definite signature of heavy metal contamination in native organisms of Cochin estuary.

$\bf{Highlights}$

$\bullet$ The tissue-specific bioaccumulation and metal selectivity index (MSI) of E. suratensis and V. cyprinoides revealed significantly higher accumulation of Cu and Zn compared to Pb and Ni throughout the study with higher rates during non-monsoonal periods.

$\bullet$ The histopathological studies in fish, E. suratensis from field conditions portrayed significant histopathological alterations such as hyperplasia, deformed secondary lamellae in gill tissues; melanomacrophage centres and necrotic lesions in liver.

$\bullet$ The estimation of human health risk assessment of heavy metals (Cu, Zn and Pb) of E. suratensis from Cochin estuary denoted a possible risk from consumption of fishes from the Cochin estuary.