Abstract Despite numerous urban pollution sources, research on aquatic species bioaccumulation in the Han River is scarce. In this longitudinal study, we assessed baseline heavy metal (HM) concentrations in Cyprinidae, a major freshwater fish family in the Han River. Specifically, were evaluated copper (Cu), total mercury (THg), cadmium (Cd), lead (Pb), and chromium (Cr) levels in the muscle of common carp, crucian carp, and barbel steed. Common carp had the highest HM accumulation, with baseline concentrations of Cu, THg, Cd, Pb, and Cr at 0.877, 0.060, 0.003, 0.032, and 0.178 mg/kg, respectively. Larger fish exhibited greater bioaccumulation, with THg levels significantly correlated with fish length (correlation coefficients: 0.57 (p < 0.05)–0.74 (p < 0.001)). Notably, Cr accumulated more extensively in fish muscle than Pb, and the metal selectivity index (MSI) of THg in barbel steed was 2–3 times higher than in other fish species. The baseline concentrations determined in this study can serve as identifiers of the initial point of abnormal HM bioaccumulation in fish and provide foundational data for future long- or short-term fish monitoring.