Burrowing mayflies (Ephemeroptera: Ephemeridae) are sensitive to pollution and have been used as environmental indicators in the Great Lakes. Hexagenia limbata and Ephemera simulans population abundance and biomass estimates from Chequamegon Bay, Lake Superior, were compared between the years 2002 and 2012 as well as inside and outside the Northern States Power Lakefront Superfund site. Mean abundance was similar and mean biomass of Ephemeridae was slightly less in 2012 than in 2002, most likely due to the occurrence of E. simulans in 2012, a smaller species not collected in 2002. In 2012, mean ephemerid abundance and biomass outside the Superfund site was significantly higher than inside the Superfund site. Biomass was higher in clay, clay with sand, and sand with clay substrates than in fine sand, coarse sand, or wood debris substrates. Substrate in the Superfund site was predominantly wood debris. Future monitoring of ephemerid populations in Chequamegon Bay, and particularly in the Superfund site as clean up begins, would be valuable to establish long-term population trends for these two species and potentially shed light on the habitat requirements of E. simulans, an understudied species in the Great Lakes.