Urban river runoff carrying various anthropogenic sources of heavy metals (HMs) is the most important input pathways for HM pollutions in the coastal region, apportioning sources of environmental pollutants is key to controlling coastal HM pollution. In the study, surface sediments were collected from seven urban rivers flowing through Lianyungang City and discharging into Haizhou Bay, Eastern China. The concentrations of HMs of the river sediments were, in mg/kg (mean value ± standard deviation): Mn (550 ± 227) > Zn (67 ± 61) > Cr (33 ± 12) > Ni (21 ± 8.5) > Cu (16 ± 7.6) > Pb (15 ± 5.6) > Cd (0.11 ± 0.06), which were slightly to moderately polluted. As important outlets for municipal and industrial sewages, the Shawang River and Linhong River were the most polluted. Based on the multivariate statistical analysis, HMs were attributed to anthropogenic source (industrial, domestic, and agricultural discharges) and natural source (soil parent materials and atmospheric deposition). Based on isotope source apportionment, Pb was mainly from natural source, exhausts of leaded gasoline vehicles, and coal combustion, with the mean contributions of 39.3%, 23.7%, and 37.0%, respectively, and Sr originated from natural source and anthropogenic source, with mean contributions of 31.8% and 68.2%, respectively. Pb-Sr isotopes illustrated that anthropogenic inputs were the dominant source for HMs in urban river sediments flowing into Haizhou Bay, and the isotope tracing results make up the discriminating deficiency of the multivariate statistical analysis.