In the process of industry modernization, the manufacturing industry became an industry with intensive water pollution emissions. The major water pollutants discharged by the manufacturing sector in the Yangtze River Delta (YRD) accounted for more than 20% of the national total in China. The gross sales value of manufacturing industries in the YRD accounted for nearly 30% of the national gross sales value. Therefore, it is necessary to accurately identify the types of water pollution-intensive industries (WPIIs) in regions with developed manufacturing industries and water networks like the YRD in China, and analyze the spatial-temporal evolution of manufacturing water pollution-intensive industries (MWPIIs) of the YRD for both 2018 and 2020. The comparison method is used to analyze the spatial-temporal evolution in the YRD. Through empirical research, this paper reveals a certain dislocation in the development of manufacturing clustering in the three provinces and one municipality in the YRD. However, it is found that MWPIIs predominantly fall into Large-scale and Super-intensive types, indicating that more than half of water pollution emissions from MWPIIs exhibit both high-scale and intensity characteristics. Therefore, the suggestions for development paths and integrated strategies of MWPIIs are put forward to achieve enhanced regional water environmental governance performance through collaborative environmental governance in the YRD.