The St. Mary's River, deemed a Great Lakes Area of Concern due to its degraded environmental status, has served as the site of much of Moerke's research. Moerke has studied zooplankton, Lake Sturgeon, and Atlantic salmon in the river, as well as physical conditions such as sediment quality. This included contributing to a 2010 assessment of the river's biology and hydrology for the U.S. Army Corps of Engineers, concluding that ongoing shifts in the biological community had the potential to drastically alter the ecosystem if they continued. In 2015, she performed a baseline documentation of the Little Rapids section of the river for the Great Lakes Commission and the Michigan Department of Environmental Quality. Moerke has also documented the positive effects of restoration on that section of the river, such as increased abundance and diversity of fish and benthic macroinvertebrates.
