The Karnaphuli River is one of the prime and most important streams in the southeastern part of Bangladesh. The favorable water current and the geographic location have rendered the Karnaphuly River estuary a suitable habitat and a breeding ground for diverse fish species. Reversely, this estuary has been polluted by discharges from many point and non-point sources due to its location in the catchment area of a heavily industrialized area, Chattagram port city. However, published research concerning the status of toxic and trace elements in some commercially important benthic and pelagic coastal fish species in Karnaphuli River estuary was not found in the existing literature. Therefore, it's an important field of study on the assessment of toxic and trace elements concentration in the commercially important benthic and pelagic coastal fish species and their health taxation in the Karnaphuli River Estuary. Energy dispersive X-ray fluorescence (ED-XRF) was used to quantify trace metal concentration in edible parts of the fish species. This study revealed that the rank of the trace metals concentration was as follows (mg/kg): Zn (37.1)>Mn (16.12)>V (11.16)>Cu (9.49)>Rb (5.62)>Pb (2.98)>Cr (1.59)>Co (1.17). The F-test showed that a significant difference at 95% confidence level in the distribution pattern of trace metals concentration among the examined fish species in the study area. The metal pollution index (MPI) in the muscle of fishes were found to be in the following order: L. bata>P. monodon>T. cirratus>M. bleekeri>O. pabda>H. nehereus>L. calcarifer>P. argenteus>P. paradiseus>T. toli, and the MPIs for most of the benthic fish species were higher compared to the pelagic fishes. On the other hand, the examined fish species were significantly bio-accumulative with the highest bio-accumulation factor value for benthic species. The multivariate analysis identified that the sources of the trace metals were associated with anthropogenic activities. For the human health risk assessment concern, estimated daily intake, target hazard quotient and cancer-causing risk were estimated. The results for non-cancer hazardous index values were found to be lower than unity. On the other hand, the total cancer risk data ranging from 1.24E-05 to 1.70E-05 were fallen within the range for the threshold values (1.0E-06 to 1.0E-04). However, considering the suggested values set by the environmental and regulatory agencies, it has been recommended that no significant non-carcinogenic and cancer-causing health risk for humans was seen due to the consumption of the studied fish species.