To clarify the concentration distribution characteristics of heavy metal and arsenic (As) and their ecological risks in the sediments of the Yellow River estuary and the long-term effects of the Flow-sediment Regulation Scheme (FSRS), the concentrations of six heavy metals (Zn, Cr, Ni, Pb, Cu, Cd) and As in the surface sediments of 27 stations sampled in 2012 were determined by ICP-MS and their ecological risks were evaluated by determining the potential ecological risk index (RI). The results showed that the average levels of heavy metal and As in inshore sediments were in the order of As > Zn > Cr > Ni > Pb > Cu > Cd. The spatial distributions of Cr, Ni, Cu, and Pb concentrations were consistent, and higher values were generally detected in inshore and near the Yellow River estuary, whereas lower values were observed far from the estuary and coastline. Ni, Cu, Pb, and Zn concentrations showed significantly positive correlations with clay (P < 0.05), whereas no significant correlations were observed between clay and Cd (or Cr and As) (P > 0.05). The average potential ecological risk indices of six heavy metals and As in inshore sediments generally followed the order of Cd > As > Ni > Pb > Cu > Cr > Zn. According to the RI values in the study area, 18.52% of stations were slightly ecologically hazardous, 70.07% of stations were moderately ecologically hazardous, and 7.41% of stations were strongly ecologically hazardous, which was mainly caused by Cd and As. Because of the use of agricultural fertilizers, inshore oil extraction, fossil fuel combustion, and estuarine pollutant input, the sources of heavy metals and As in inshore sediments are complex and diverse. This study showed that only the concentrations of Cd and As showed an increasing trend following long-term implementation of the FSRS, indicating that their ecotoxicological risk in inshore sediments of the Yellow River estuary should be evaluated in the future.