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Abstract Our study illustrated the ecological conditions in the rivers of Lake Taihu Basin (LTB) using an index of biotic integrity based on phytoplankton (P-IBI), and its performance was compared with the previously developed water quality index (WQI). Samples were collected seasonally at 96 sites covering the major rivers from September 2014 to January 2016. Three critical ecological indices, i.e., phytoplankton density, chlorophyll a (chl a), and Menhinick, were selected from a pool of 22 candidate indices mainly according to the correlations among indices and environmental parameters. The results indicated that the ecological status of LTB based on P-IBI was significantly different at spatial (especially between Tiaoxi and the other 5 river systems) and seasonal scales. Furthermore, the proposed P-IBI effectively identified the major environmental parameters (total nitrogen, ammonium, total phosphorus, and permanganate index) associated with each level (bad, low, and moderate). Moreover, the P-IBI was closely and positively correlated with the WQI at the spatial scale regardless of season. However, the ecological conditions were significantly worse according to the P-IBI at both the spatial (P < 0.001) and seasonal scales (P values of 0.018 in winter and < 0.001 in other seasons, respectively), and the seasonal distribution pattern differed between the two methods. Our study suggests that the P-IBI provides an essential supplement for the assessment of ecological conditions of rivers and that the selected critical indices (phytoplankton density, chl a , and Menhinick) are suitable for river ecosystems. Additionally, compared with WQI, the water quality condition was generally worse when using P-IBI, and this phenomenon requires further attention during water quality assessments, as well as different seasonal distribution patterns. Graphical abstract Unlabelled Image Highlights • Phytoplankton density, chl a and Menhinick are selected in the P-IBI establishment. • The proposed P-IBI was closely correlated with the previously developed WQI. • The P-IBI assessment results were generally worse than the WQI. • The seasonal distribution pattern differed between the P-IBI and WQI methods. [ABSTRACT FROM AUTHOR]