We sampled the phytobenthos (epibenthic periphyton) 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. 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. A pared-down version of this routine sampling continued from 2019 onward but is not included here. This dataset complements zebra mussel and zoobenthos data collected according to the same routine sampling structure, for which data is also archived with EDI.