<p>Watershed-scale stress from urbanization can negatively impact freshwater ecosystems and the services they provide, but our ability to manage these systems is limited by a lack of baseline knowledge. Halifax Regional Municipality (HRM), Nova Scotia, Canada, has the 8th fastest growing metropolitan area in Canada; hundreds of lakes are increasingly influenced by development, and most lakes in the urban-suburban core are developed to some degree. Lake monitoring in HRM has shown increased productivity in developed watersheds; however, a lack of historical context impedes lake management. Here, we establish a historical timeline through the analysis of biological indicators (subfossil chironomids) and elemental and isotopic geochemical records in a paleolimnological approach applied to three HRM lakes. We found that two lakes in residentially developed watersheds experienced a shift in chironomid taxa towards those indicative of human impact (<i>Chironomus</i>,<i> Cladotanytarsus mancus</i>-type); however, our analysis show that much of the changes observed to each lake occurred prior to recent housing development. Municipal water quality monitoring programs are limited to the last four decades, and conclusions about development resulting in eutrophication contrast with the findings of this study, where we found impacts associated with land clearance and modification of habitat pre-1900. This highlights the limitations of poor resolution “snapshot” surface water quality monitoring compared to paleolimnological methods, which can capture high resolution conditions within a lake. Our results will enable informed decisions related to restoration/remediation targets and assist in the planning and management of freshwater resources.</p>