Abstract: In May 2009and from May to June in 2010, a survey of aquatic organisms was carried out in Huntai River basin. A study using three quantitative methods for selecting reference sites and impaired sites was conducted to create the index of biological integrity (IBI) based on community data of macroinvertebrates, and to further evaluate the river health of the selected region. The three criteria included water quality parameters, habitat quality evaluation, and assessment of integrated water quality and habitat quality. When different reference and impaired sites were selected with different methods, either water quality criteria or habitat quality criteria selected more sites as reference than the integrated criteria. A significant difference was observed in constructing the IBI core metrics, as only four parameters (i.e., total taxa, EPT taxa, relative abundance of tolerant taxa, and relative abundance of clingers) were common among all three criteria. The assessment results showed that Huntai River was under better condition when assessed with either water quality criteria or habitat quality criteria, but under worse condition when assessed with the integrated criteria. Additionally, habitat quality criteria showed a higher accuracy rate (75%) than either water quality or integrated criteria (50% and 67%, respectively) in selecting the reference sites, while for the impaired sites, water quality (100%) and integrated criteria (100%) had a higher accuracy rate than habitat evaluation (89%).