Toxic metals and freshwater fish’s metalloid contamination are significant environmental concerns for overall public health. However, the bioaccumulation and sources of metal(loids) in freshwater fishes from Bangladesh still remain unknown. Thus, the As, Pb, Cd, and Cr concentrations in various freshwater fish species from the Rupsha River basin were measured, including Tenualosa ilisha, Gudusia chapra, Otolithoides pama, Setipinna phasa, Mystus vittatus, Glossogobius giuris, and Pseudeutropius atherinoides. An atomic absorption spectrophotometer was used to determine metal concentrations. The mean concentrations of metal(loids) in the fish muscle (mg/kg) were found to be As (1.53) > Pb (1.25) > Cr (0.51) > Cd (0.39) in summer and As (1.72) > Pb (1.51) > Cr (0.65) > Cd (0.49) in winter. The analyzed fish species had considerably different metal(loid) concentrations with seasonal variation, and the distribution of the metals (loids) was consistent with the normal distribution. The demersal species, M. vittatus, displayed the highest bio-accumulative value over the summer. However, in both seasons, none of the species were bio-accumulative. According to multivariate statistical findings, the research area’s potential sources of metal(loid) were anthropogenic activities linked to geogenic processes. Estimated daily intake, target hazard quotient (THQ), and carcinogenic risk (CR) were used to assess the influence of the risk on human health. The consumers’ THQs values were < 1, indicating that there were no non-carcinogenic concerns for local consumers. Both categories of customers had CRs that fell below the permissible range of 1E − 6 to 1E − 4, meaning they were not at any increased risk of developing cancer. The children’s group was more vulnerable to both carcinogenic and non-carcinogenic hazards. Therefore, the entry of metal(loids) must be regulated, and appropriate laws must be used by policymakers.