Extensive research has occurred at Waubesa Wetlands over the years. Principally, two emeriti professors from the University of Wisconsin - Madison have been instrumental in compiling and promoting information about the Wetlands. The book Waubesa Wetlands: New Look at an Old Gem by Joy Zedler highlights unique aspects of the Wetlands, drawing on her own research experience as well as on those of researcher Calvin DeWitt. The book contains an extensive reference list offering additional information.

In 2018, a UW-Madison project conducted ecosystem services assessments, water quality monitoring, modeling, and community engagement activities within the Waubesa Wetlands watershed. From these activities, the group developed management recommendations.