Where carbonate bedrock aquifers are overlain by complex glacial sediments, these sediments control the locations and geochemical signature of recharge to the bedrock groundwater system. In these settings, geochemical and isotopic tracer tools that have traditionally proven effective for characterizing hydrochemical evolution in carbonate bedrock aquifers may be rendered ineffective due to geochemical fingerprinting that can develop as groundwater migrates through the sediments of the recharge pathway. Traditional tracer tools are assessed in an 8,000 km2 study area in the Early Silurian carbonate aquifers of southern Ontario, Canada. These carbonate aquifers contain significant quantities of high-quality groundwater resources and provide the sole drinking water source to many large cities and private residences. The glacial history of the study area is complex, with the advance and retreat of three ice lobes having deposited sediments that vary widely in permeability, lithology and geochemistry. Results show that spatial trends of higher tritium corroborate with aerobic redox chemistry in the carbonate groundwater systems underlying areas of thin or permeable sediment cover. Groundwater chemical evolution beyond recharge areas is assessed with general chemistry, redox characteristics and an investigation of water-rock interaction. A comparison of strontium isotope ratios (87Sr/86Sr) in bedrock and groundwater shows that long residence times may be required for the isotopic signature of the carbonate bedrock to imprint on the groundwater, though this does not occur consistently. Sulphur isotopic composition (34S and 18O stable isotopic signatures of sulphate) in groundwater was most informative, showing isotopic evidence of pyrite oxidation in recharge areas, and a Silurian sulphur isotopic signature of the host bedrock in areas of thick and low permeability sediments, downgradient of identified recharge areas. The set of tracer tools deemed most useful in this investigation provides the empirical evidence needed to support a conceptual model of recharge and groundwater evolution and is recommended for use in similar settings elsewhere.