Macroinvertebrates as a biological indicator of aquatic health condition plays an important role in the protection and management of water ecological environment. Macroinvertebrates and water quality were investigated on the basis of samples collected at 33 sampling sites in the North Canal River Basin in May 2015. The community structure of macroinvertebrates was analyzed. The comprehensive water quality identification index and Biotic Index of macroinvertebrates were used to assess the water quality in the North Canal River Basin. The results obtained by using these two methods were compared each other by using the Kolmogorov-Smirnov test and Pearson correlation analysis. In this study, a total of 23 species of macroinvertebrates belonging to 3 phylum, 4 class, 6 order, 11 family and 11 genera were identified in the North Canal River Basin, which mainly represented by aquatic insects and molluscs. The community structure of macroinvertebrates in the whole basin was simple. The result of Biotic Index showed that 72% of the sampling sites were moderately(Ⅳ) or seriously(Ⅴ) polluted and comprehensive water quality identification index showed that more than 57% of the sampling sites were worse than Class Ⅳ. The K-S test showed that the results were confirmed to normal distribution and Pearson correlation analysis exhibited that the results of these two methods had a significant positive correlation. The two results had the same tendency generally. Depending on the results, the water quality in the North Canal River Basin was poor. The main stream was better than the tributaries and the upstream was better than the downstream. The water quality in the upstream of the Wenyu River, the downstream of the Ba River, the upstream of the Tonghui River and the Liangshui River were poor while the headwater of the Wenyu River and the upstream of the Ba River were excellent. The result of comprehensive water quality identification index was a little better than that of Biotic Index. This was attributed to the reason that the two assessment methods focused on different spatial and temporal scales. In the North Canal River Basin with high urbanization level and strong human disturbance, the complex water ecological condition could be better understood with both assessment methods at the same time.