The construction of ecological civilization is a major national strategy for the new era. The development philosophy of “lucid waters and lush mountains are invaluable assets” has taken deep root among the people. Water security guarantee, environmental pollution control, geological disaster prevention and control, as well as water and soil resources protection constitute the core tasks of ecological civilization construction. The advancement of these tasks relies on the in-depth integration and coordinated efforts of water, environment and geology disciplines. Against this background, an in-depth exploration into the training paths for interdisciplinary innovative and applied talents in the fields of water, environment, and geology can not only improve the talent training quality of universities, but also provide solid talent support for China’s ecological civilization construction and resource and environment governance, which possesses important practical significance and application value. This paper first elaborates the core value of cultivating interdisciplinary innovative and applied talents majoring in water, environment, and geology, and then puts forward a set of effective training paths, aiming to offer references for relevant researchers.