Dr. Johengen is a research scientist and Associate Director 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, controlling the introduction of invasive species, and development of in situ water quality sensors and observing systems.

Current research projects include impacts of multiple stressors on the Saginaw Bay, Lake Huron ecosystem, Application of Brine Treatments for controlling non-indigenous species introductions associated with shipping activities, Implementation of the Great Lakes Observing System, Monitoring Long-trem trends in the lower food web of the Great Lakes, Examining Causes and Consequences of the decline of Diporeia in the Great Lakes.