[Aim] As one of the oldest industrial bases in China, the Songhua River has been seriously damaged, and environmental protection is facing huge challenges. Therefore, it is urgent to carry out studies on water quality and the diversity of benthic macroinvertebrates.[Method] In July 2016, the macroinvertebrate communities in the Songhua River were investigated, together with the water quality indicators and biological indices. Furthermore, the relationship between community structure and environmental factors was analyzed by redundancy analysis.[Result] Three stream segments of the Songhua River showed different environment gradients. Based on the single factor water quality assessment, the southern Songhua River was in moderate pollution and the water in the northern Songhua River was not seriously polluted. The water quality of a tributary branch, the Wutong River had the best water quality. The geographical distribution of benthic macroinvertebrates varied greatly in the different zones. The species diversity of the Wutong River was the highest, followed by the northern Songhua River, and it was the lowest in the southern Songhua River. The redundancy analysis (RDA) showed that dissolved oxygen (DO) and potassium (K) concentrations were the leading factors driving the patterns of benthic macroinvertebrates communities. Based on two biological indices, all three stream segments in the Songhua River were slightly polluted.[Conclusion] The water of the Songhua River had light-to-moderate pollution levels. Furthermore, organic pollution was the main environmental problem, which influenced the benthic macroinvertebrate communities. Therefore, further efforts should be made to control the input of organic pollution in order to keep acceptable water quality in the Songhua River.