Contamination of estuarine fish with trace elements (TE) is a growing concern globally. This study assessed six commonly consumed fish species (Hilsa ilisha, Acanthopagrus latus, Mugil curema, Glossogobius giuris, Lates calcarifer, and Harpodon nehereus) for trace elements (TE) pollution levels, and health risks related to consumption from a subtropical estuary along the Bay of Bengal Caost. Fish samples collected in dry (March 2020) and wet (August 2020) season from five sites were analyzed for As, Cd, Cr, Ni, and Pb using Flame Atomic Absorption Spectrometer (FAAS). The average concentration of As, Cd, Cr, Ni and Pb was 0.45 ± 0.23, 0.05 ± 0.03, 0.65 ± 0.36, 0.29 ± 0.16 and 1.35 ± 0.72 mg/kg which were within Food and Agricultural Organization (FAO)/World Health Organization (WHO) reference values. The concentration of TE was ranked in a decreasing order of Pb > Cr > As > Ni > Cd. As and Pb content was the maximum in L. calcarifer and Cd, Cr and Ni in H. nehereus. Concentration of all the TE was varied significantly among the fish species except for Cd. Principal component analysis (PCA) and clustering analysis (CA) indicated a general distribution of the elements and they possibly originated from anthropogenic sources. The Average Pollution Load Index (APLI) ranged from 0.84 to 1.95, with M. curema, G. giuris, L. calcarifer, and H. nehereus exceeding the critical threshold of ‘1’, indicating severe pollution. The estimated daily intake of 0.0002–0.0003 mg/kg/day for children consuming Pb contaminated fish was above the recommended limit. The non-carcinogenic risk (THQ) for As and Pb also exceeded acceptable thresholds, suggesting significant health risks for children. Although carcinogenic risk (CR) values were within acceptable limits for most metals, the potential risk remains, particularly for children. These findings are highlighting the varying contamination risks among fish species and the higher risk for children.