A new approach by combining bioindicators (BiI) and biotic indices (BIs) for evaluating water quality is presented in this paper. It is then applied to the Huai River Basin (HRB), China, which is well-known globally for its heavy anthropogenic influences. Results indicate that the spatial distribution of BI-indicated water quality has roughly the same pattern as that shown by BiI, but the pollution level using BI was, on average, greater than that by BiI; the northern plain area has a degraded water quality (ranging from ‘α-mesosaprobic’ to ‘α-polysaprobic’ in a wet season) while the southern mountain area and the southern part of the East Line of the South–North Water Transfer Project has a better water quality (‘β-mesosaprobic’). Water quality is worse in the dry season than in the wet season. We concluded that zoobenthos and zooplankton are more reliable indicators of water quality; biological indices are more sensitive to water quality but less reliable than BiI. These results will be of use in the ecological restoration of the Huai River and benefit water resource management in HRB in the future.