A sequential extraction procedure was applied to determine the concentration and fractionation characteristics of eight heavy metals (HMs) (Cu, Zn, Pb, Cd, Cr, Fe, Mn, and Ni) in a sediment core collected from the old Yellow River Estuary, China. The results revealed that the mean deposition rate of this sediment core, which spanned 87 yr (1925–2012), was approximately 0.5 cm yr−1. The mean concentrations and ranges of HMs were Cu: 26.9 (18.3–38.5), Zn: 76.4 (51.0–107), Pb: 37.3 (17.8–53.8), Cd: 0.23 (0.20–0.27), Cr: 84.7 (45.5–116), Fe: 24,000 (16,500–31,700), Mn: 709 (388–1020), and Ni: 36.1 (24.8–47.2) mg kg−1 (dry weight). Six HMs (Cu, Zn, Cr, Cd, Fe, and Ni) were present in their highest proportion in the residual fraction; their lowest proportion was observed in the exchangeable fraction. Lead primarily existed in the oxidizable or residual fraction. Manganese was mainly presented in the exchangeable fraction. The risk assessment code results revealed that the sediments displayed a low risk for Cu, Zn, Pb, Cr, Cd, Fe, Mn, and Ni. The HMs Cu, Zn, Cr, Cd, Mn, and Ni displayed minor enrichment in the sediment core, whereas for Pb, moderate contamination enrichment was observed. Overall, an increase in Igeo and total concentration of HMs occurred since 1925 and reached a maximum value around 1980, after which there was a larger fluctuation or decline until 2012. We also found that the degree of HM pollution during the 1976–1996 period was less serious than before 1976. All the sediment samples exceeded the effect range low (ERL) for Ni, whereas 56.1, 7.32, and 17.1% exceeded the ERL values for Cr, Cu, and Pb; no samples exceeded the ERL for Zn or Cd.