Dr. Johengen is a Limnologist who oversees the research activities of the Cooperative Institute for Limnology and Ecosystems Research (CILER), which is a NOAA Joint Institute program at the University of Michigan with the NOAA-Great Lakes Environmental Research Laboratory serving as the host lab. CILER's research activities are focused around five themes including: Climate and Large-Lake Dynamics, Coastal and Nearshore Processes, Lare-Lake Ecosystem Structure and Function, Remote Sensing, and Marine Environmental Engineering. Dr. Johengen's individual research interests focus on nutrient cycling and lower food-web dynamics in the Great Lakes.

Current research projects include ecological impacts of non-indigenous species on nutrient cycling and water quality, control of non-indigenous species introductions associated with shipping activities, and influence of episodic events on biogeochemical coupling of sediment nutrient fluxes and microbial production in the Great Lakes.