Many drinking water reservoirs in eastern Canada are experiencing recovery from acid deposition, resulting in increased water-column biological activity. Pockwock Lake, the primary drinking water supply for the City of Halifax, Nova Scotia, has experienced increased pH and NOM resulting in treatment challenges and increased operating costs. Halifax Water has been collecting chemical water quality data throughout the lake and tributaries since 2008, however water-column biological activity in Pockwock Lake is not well-characterized. We analyzed a dated lake sediment core for historical zooplankton (Cladocera) abundance in combination with previously-obtained sedimentary diatom abundance data to evaluate historical water-column biological activity. A significant change in Cladocera assemblages throughout the Pockwock core is present, corresponding with acidification and lake recovery trends. Environmental DNA (eDNA) is used to complement bio-proxies and expand the range of organisms detectable in lake sediments. The combined use of the subfossil morphological identification and sequenced genes can provide powerful results which can inform long-term planning, monitoring and management of drinking water reservoirs.