The distribution as well as the spatial and temporal variation of total phosphorus(TP)in the water and sediment, and the heavy metals in the sediment in the main stream of Huaihe River were studied. Samples of water and sediments in 19 sections of the main stream of Huaihe River from the Zhengyangguan to the Hongze Lake were collected from 2014 to 2017. The TP in the water and sediment, and heavy metals(As, Cu, Pb, Zn, and Cd)in the sediment were analyzed to investigate the concentration and distribution along the river. The effects of the flow rate and temperature on the spatial and temporal distribution of the TP in water and sediment, and heavy metals in the sediment were also discussed. The results showed that the concentration of the TP and heavy metals during pre-flood season is more than that after flood season, and the distribution of various forms phosphorus in water during flood season is more uniform. The flow rate and temperature are main influencing factors for this distribution of TP and heavy metals.