The Taihu Basin is facing problems such as the increasing difficulties in continuously improving the lake’s water quality and an ineffective aquatic ecological system. To solve these problems, an ecological investigation was conducted at 87 sites in the Taihu Basin in wet, normal, and dry seasons from 2012 to 2013. The results show that benthic organisms at 53% of the sites, phytoplankton at 65% of the sites, and zooplankton at 35% of the sites were at low levels as evaluated by the Shannon-Wiener index. Non-point source pollution has become increasingly prominent, with COD, NH₃-N, TP, and TN accounting for 53%, 46%, 68%, and 45%, respectively, of the total amount of pollutants in the lake. The project lacked a long-term operation and management mechanism, with less focus placed on the operation management and more focus placed on the project construction. Several countermeasures are put forward: (1)establishing aquatic ecological function regionalization and restoring the integrity of the ecosystem, (2)strengthening the control and management of non-point source pollution and rural black and malodorous rivers, (3)setting strict standards for the discharge of pollutants, and(4)improving the operational management of the project.