Contaminants in overlying water and sediments of 19 sections from Zhengyangguan to Laozishan in the main stream of Huaihe River were sampled for seven times from 2014 to 2017. The total phosphorus(TP)and main heavy metals, such as As, Cu, Pb, and Zn, in the overlying water and sediment were analyzed to reveal the spatial and temporal distribution characteristics and their main influence factors, and then, this study evaluated the environmental effect for each pollutant. The results show that the concentration of contaminants in the sediment in November is lower than that in June. Meanwhile, the concentrations of various contaminants are decreasing with time, especially TP and As. The analysis of pollutant sources shows that TP in the sediment is affected by the non-point source, while heavy metals are affected by the point source. TP and four heavy metals in the sediment of Huaihe River do not have ecological risk within the monitoring range.