We sampled the zoobenthos (macroinvertebrates of the benthos) of Lake Mendota from 2016-2018 to track impacts of invasive zebra mussels (Dreissena polymorpha) which were discovered in Lake Mendota in 2015 and grew exponentially to densities greater than 10,000 m-2 in shallow, rocky habitat by 2018. The data presented here exclude all zebra mussels, which are archived in a separate datset. We sampled along three transects inherited from Karatayev et al. (2013) at five different depths (1, 3, 5, 8, and 10 m) twice a summer (June and August) from 2016-2018. These data also contain some samples opportunistically taken from deeper depths along these transects that do not follow the routine sampling structure. A pared-down version of this routine sampling continued from 2019 onward but is not included here. This dataset complements zebra mussel and phytobenthos data collected according to the same routine sampling structure, for which data is also archived with EDI.