<p>Lake Taihu, the largest shallow freshwater lake in eastern China, is a vital ecological and economic resource in the Yangtze River Delta. However, the region faces substantial environmental challenges from emerging contaminants (ECs), such as per-and polyfluoroalkyl substances (PFAS) and neonicotinoid insecticides (NEOs), driven by its dense industrial activities and aquaculture and agriculture sectors. A comprehensive literature analysis of the two ECs revealed that PFAS and NEOs have become recent hotspots both globally and in the Taihu Basin. The occurrence and distribution of PFAS and NEOs were summarized to show their high detection frequency and concentrations in the Taihu Basin. Risk assessment indicated that PFAS, NEOs, and other ECs posed considerable ecological risks within the Taihu Basin. Treatment techniques for PFAS and NEOs were systematically reviewed. However, many of these techniques face difficulties in scaling up in the Taihu Basin because of their strict conditions and high energy consumption. Ecological engineering treatment technologies are applied in the Taihu Basin to address emerging agricultural contaminants. Ecological engineering treatment technologies have limitations such as low removal efficiency and toxicity inhibition. Thus, it is necessary to develop more effective technologies for treating ECs in the Taihu Basin. A flowchart for identifying priority controlled ECs is presented and a future for the priority controlled emerging contaminants in the Taihu Basin is discussed. This study provides scientific insights for the sustainable control of ECs.</p>