Toxicity bioassays measure the direct impacts of contaminants on aquatic environment. Sediment toxicity bioassay using resident species with analysis of priority chemicals accomplish the reliable risk assessment. Copepods are sensitive to environmental contaminants and widely applied for toxicity bioassays. Therefore, present study demonstrates sediment toxicity bioassay on meio-benthic harpacticoid copepod Tisbe furcate. Sediment quality parameters, metals, and total petroleum hydrocarbons (TPHs) are measured in the sediment. Pollution load index (PLI) and potential ecological risk index (PERI) are determined from metal concentration. Biological responses of copepod and sediment microbe are measured by hydrolysis of fluorescein diacetate (FDA). Sediment quality is assessed by the rate of FDA hydrolysis in comparison with sediment quality parameters. Absorbance of fluorescein in sediment extracts measured between 0.0437 and 0.0846 by copepods. Sediment toxicity response of copepods exhibited that the estuarine sediments are highly toxic with considerable ecological risk attributing higher PLI and PERI respectively. Interestingly, the toxicity bioassay exhibits moderate toxicity in the sediment samples of bar mouth and off-shore of the estuary. However, PLI and PERI reveal that these sediments are unpolluted with low ecological risk and even the impact from unknown emerging contaminants can be captured by sediment toxicity using copepod. High hydrolytic activities by sediment microbes at main stream of estuary and coastal sediments are attributed to sewage discharges. These assays are more environmentally relevant, reliable and cost-effective, and numerous tests can be conducted with basic laboratory equipments to regulate pollution.

$\bf{Highlights}$

$\bullet$ Sediment toxicity bioassay on benthic copepod captured impact of pollutants.

$\bullet$ FDA hydrolysis by microbe can be used to assess the level of fecal contamination.

$\bullet$ Sediment toxicity bioassay accomplishes the ecological risk assessment.

$\bullet$ Bioassay described is rapid, inexpensive and aids reliable risk assessment.

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.