The cost of surface water treatment is directly impacted by changes in metal concentrations, dissolved organic carbon, and other water quality parameters within surface water reservoirs. Water utilities build infrastructure for multi-decadal life cycles, where there is seldom a multi-decadal water quality record from which to assess long-term variability. Lake sediment has long been used to assess long-term variability in surface water quality, and has been used to obtain information about inter-annual to centennial scale changes that predate the monitoring record in drinking water reservoirs. Using 10 sediment cores collected from 6 water supply reservoirs near Halifax, Nova Scotia, we demonstrate the utility of a lake sediment approach to long-term water quality variability in the context of water supply management. The methodology used was designed to be a cost-effective, accessible, and applied approach to well-established limnological methods. Our results indicate that these methods were able to (1) assess the magnitude of past water quality variability in all reservoirs, (2) suggest additional water quality parameters that should be measured based on sedimentary metal concentrations, and (3) suggest probable future trends in dissolved organic carbon based on stable isotopes of carbon and nitrogen. Collectively our data suggest a set of limnological techniques, sediment analyses, and data management strategies that together form a preliminary framework with which to apply lake sediment analysis to the assessment of drinking water reservoirs.