This study was based on surveys of zoobenthos in the Songhua River during summer and autumn 2008 to provide baseline information for future regulations on water quality. Based on the Shannon-Weaver diversity index, the Margalef richness index, the Simpson biological index and the Goodnight-Whitely modification index, water quality was categorized based on zoobenthos assemblages. In summer, 21 species of zoobenthos were recorded: 8 aquatic insect larvae, 10 mollusks and 6 annelids. In autumn, 24 species of zoobenthos were recorded: 11 aquatic insect larvae, 9 mollusks and 4 annelids. During the summer, zoobenthos densities ranged from 16 to 3200 organisms/m2, averaging 723 organisms/m2, while biomass ranged from 0 to 106 g/m2, averaging 26 g/m2. During the autumn, zoobenthos densities ranged from 16 to 6368 organisms/m2, averaging 1321 organisms/m2. Biomass ranged from 0 to 92 g/m2, averaging 31 g/m2. The study has important practical significance, as it shows the possibility to monitor and evaluate aquatic bio-indicators reflecting the water quality of Songhua River.