With its myriad of lakes, the Kenauk property is an exceptional location for aquatic surveys and research projects. To accomplish this, the Kenauk Institute offers a wide range of boats and vessels to its researchers and guests, consisting of non-powered crafts (e.g., kayaks, canoes) and powered crafts (electric or gas motor).

Note that the availability and type of craft depends on the lake being used and whether the operator has their boating license. To prevent the introduction and spread of invasive species, Kenauk does not allow the entry of any outside boats.  Additionally, all research equipment must be decontaminated before entering the Kenauk property, as well as when being moved between Kenauk lakes.