Dr. Johengen is an Associate 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: NOAA-CSCOR, Impacts of multiple stressors on the Saginaw Bay, Lake Huron ecosystem; NOAA-IOOS, Alliance for Coastal Technologies; NOAA-IOOS, Implementation of the Great Lakes Observing System; USEPA, Monitoring Long-trem trends in the lower food web of the Great Lakes; GLFT, Examining Causes and Consequences of the decline of Diporeia in the Great Lakes.