The concentrations of heavy metals (Cr, Ni, Cu, Zn, Pb, Cd) and arsenic (As) in the water and suspended particulate matter (SPM) of different layers of the tail reaches of the river and estuary (low-salinity area) of the Yellow River were sampled in the pre-flood (April) and post-flood (October) seasons of 2016 to investigate their distributions in a seaward direction. The ecological risk of heavy metals and As in the water and SPM of different depth layers were evaluated. The results showed that in the pre-flood season, only the mean level of Cd in the surface layer was higher in the tail reaches than in the low-salinity area, whereas the average concentrations of As, Cr, Cu, Ni, and Pb in the bottom layer water were higher in the tail reaches than in the low-salinity area. In the post-flood season, the average level of Ni in the surface water layer was lower in the tail reaches than in the low-salinity area, while the average concentrations of the six heavy metals and As in the bottom layer were higher than those in the low-salinity area. Moreover, in the pre-flood season, the average concentrations of As, Cd, Cu, Ni, Pb, and Zn in SPM in the surface layer were lower in the tail reaches than in the low-salinity area and the average levels of six heavy metals and As in SPM in the bottom layer of tail reaches were all lower than those in low-salinity areas. In the post-flood season, the average concentrations of six heavy metals and As in SPM of the surface layer of tail reaches were higher than those in low-salinity areas; the average levels of As, Cd, Cr, Cu, and Pb in SPM of the bottom layer were higher in tail reaches than in low-salinity areas. As and metal pollution in the water of surface and bottom layers of tail reaches and low-salinity areas was not serious, and was generally in accordance with the Class I Criteria of Environmental Quality of Surface Water in China and the Class I Criteria of Seawater Quality in China, respectively. Compared with the pre-flood season, the sum of toxic units (ΣTUs) and the mean probable effects level (PEL) quotient of As and metals in the SPM of the surface and/or bottom layers of tail reaches and low-salinity areas decreased greatly in the post-flood season, indicating that the implementation of a Flow-Sediment Regulation Scheme during the flooding season could reduce the potential ecological toxicity risk caused by the combined effects of these elements in suspended particles.