Abstract: Water and suspended substance are the main carriers for the migration of heavy metal elements in rivers. The paper systematically studies the distribution characteristics of heavy metals in suspended substance and filtered water from the middle and lower reaches of Nenjiang River. The results show that the migration of suspended substance mainly occurs in wet season, and the inflow of tributaries may affect the concentration of suspended matter in the main stream. The industrial and domestic activities in Da'an City have obvious influence on the concentration of suspended matter; while those in Qiqihar have little influence on the heavy metal contents in suspended substance, but significant influence on Cr, Cu, Pb, Ni, and Zn in water. Yalu River brings the most heavy metals Cr and Ni to Nenjiang River, with the annual flux of 1223 and 100.46 t, respectively. Arun River inputs the most heavy metals Cd, Cu and Pb, with the annual flux of 0.08, 10.93 and 9.96 t, respectively. The annual fluxes of heavy metals such as As, Hg, Cd, Cr, Cu, Pb, Zn and Ni from Nenjiang River to Songhua River are 113.7, 0.32, 0.79, 438, 164, 152, 440 and 224 t, respectively.