Students may choose between the MS in Environmental Engineering or the MS in Civil Engineering with a concentration in Environmental and Water Resources Engineering. The MS in Environmental Engineering is more closely aligned with the program's roots in process engineering and therefore requires students to have taken at least one graduate-level course in this area. The MS in Civil Engineering is the degree option that should be taken by students not interested in studying process engineering.

Students in both MS programs conduct research on topics including water resources, climate change, environmental microbiology, and biotechnology. They also have access to cutting-edge facilities, a wide range of advanced instrumentation, and mentorship from award-winning faculty.

In addition to the traditional 2-year research-based option, the program offers a 1-year coursework-based option. The research option is typically followed by students receiving financial support in the form of a research or teaching assistantship. The coursework option is designed to be completed in 9–12 months. Students pursuing the latter option may only receive partial financial assistance.