In recent years, with the steady progress of ecological civilization construction in China, “Water Pollution Control Engineering,” as a core course of environmental engineering, has become increasingly important. Ideological and political education in courses emphasizes integrating ideological and political education into the entire teaching process, aligning knowledge transmission and value guidance to move in the same direction, and effectively addressing the problem of “separation between ideological and political education and professional education”. However, the ideological and political construction of “Water Pollution Control Engineering” still faces challenges such as rigid and single teaching methods, unsystematic ideological and political elements, and imperfect evaluation systems. As a result, the course cannot give full play to its due educational function, and it is difficult to improve the teaching quality of Water Pollution Control Engineering comprehensively. In response, this paper first analyzes the dilemmas in the ideological and political construction of “Water Pollution Control Engineering,” and then puts forward corresponding solution strategies, so as to provide certain references for relevant researchers.