The traditional professional agglomeration of manufacturing and the diversified agglomeration based on the upstream and downstream correlation of the industrial chain investigated. 26 prefectural cities in the Yangtze River Basin are selected as typical representatives to compare and analyze the impact of manufacturing on water pollution in the Yangtze River Basin under the two types of agglomeration conditions. The results show that: In the whole samples, the professional agglomeration of manufacturing industry and the diversified agglomeration of upstream and downstream industries can reduce water pollution, and the pollution reduction capacity of professional agglomeration is greater than that of upstream and downstream industries. The pollution reduction capacity of the upstream diversified agglomeration of manufacturing industry is greater than that of the downstream diversified agglomeration. The water pollution in the upstream of the Yangtze River Basin will aggravate the water pollution in the downstream. The impact of professional agglomeration of manufacturing industry on water pollution in the basin exhibits the characteristics that the downstream cities have the strongest pollution reduction capability, the upstream cities take the second place, and the cities in the middle reaches are the weakest. The diversified agglomeration relates to the upstream and downstream correlation of the manufacturing industrial chain has a better effect on reducing water pollution in the downstream than that in the middle and upstream reaches. Therefore, under the background of strong path dependence between professional agglomeration and diversified agglomeration, attention should be paid to the industrial layout and pollution control in the upstream reaches of the Yangtze River Basin.