Graduate environmental engineering education builds on traditional engineering components, typically found in departments of biological and agricultural, civil, and chemical engineering. 

The breadth and multidisciplinary nature of environmental problems requires that environmental engineers possess skills beyond those normally associated with a single engineering field. Knowledge in geology, hydrology, soil and Land Resources, computers, microbiology and water, atmospheric chemistry, and other disciplines provides breadth to enhance technical skills. Good communication skills are also essential.

The College of Engineering offers M.S. (thesis) and M.Engr. (non-thesis) environmental engineering (EnvE) degrees at the Moscow and Idaho Falls campuses. The interdisciplinary program combines the resources of three departments (Biological and Agricultural Engineering, Chemical Engineering, and Civil Engineering) to provide a solid design-based environmental engineering curriculum. 

Environmental engineering research is actively supported both externally and by several interdisciplinary centers on campus including the Idaho Water Resources Research Institute, the Center for Hazardous Waste Remediation Research, the Environmental Research Institute, and the National Center for Advanced Transportation Technology.

The College of Engineering collaborates with environmental engineering faculty from Washington State University, located just eight miles west of Moscow, in research, cooperative courses, and seminars. The Idaho Falls program is coordinated with Idaho State University's master's program in environmental engineering.