Nemerow index method and benthic index of biological integrity method have been used to evaluate the water quality and the health status of aquatic organisms in Taihu Lake during 2008-2012, respectively. The results showed that the water in the whole Taihu Lake was polluted, and the aquatic organisms were basically kept in sub-health state. The results of the water quality and aquatic biological assessment exhibited generally the same trend at a large scale. In the view of the whole lake, the water quality and aquatic health status in East Taihu Lake were better than those of the other parts. In the view of time, the water quality and aquatic health status during 2008-2010 were worse than those of the lake in the 1960s. The results observed from the two assessment methods were not the same during short periods of time and in some special sample points, which were attributed to the following reasons: (1) the two assessment methods focused on different time scales and (2) the aquatic biological health status was related to the water quality as well as the environmental habitat. Since organic pollutants and excessive nutrients were the main factors influencing the water quality and aquatic health status, reducing the concentrations of the organic pollutants and inorganic nutrients should be a feasible method to improve the water quality and the ecological function of Taihu Lake.