Major shifts in hydroclimate have been documented during the last deglacial period and the Holocene in south‐central Alaska. Rare freshwater calcium carbonate (marl) deposits in lakes on the Kenai Peninsula can be used to reconstruct past changes in hydroclimate, including the influence of groundwater inflow to lakes. Here, the postglacial sediment sequence from groundwater‐fed Kelly Lake (60.514°N, 150.374°W) was analyzed for multiple proxies including isotopes of carbon and oxygen in marl calcite (δ13Cmarl and δ18Omarl), and isotopes of carbon (ẟ13COM) and abundances of C and N in organic matter. Bulk sediment analyses include organic matter and calcium carbonate (CaCO3) contents, visual stratigraphy and sediment flux. These analyses extend those of a previous paleoenvironmental reconstruction from Kelly Lake, which focused on sedimentary diatom oxygen isotopes and mass balance modeling over the past 10 000 years. Here, we show that Kelly Lake was deglaciated prior to 14.6 ka, and that by 14.0 ka marl dominated the sediments, with CaCO3 precipitation probably driven by groundwater input and mediated by shallow‐water charophytes. Marl accumulation decreased as organic and clastic inputs increased between ~12.2 and 11.5 ka. This shift, together with an increase in both δ13Cmarl and δ18Omarl values and a decrease in CaCO3 content, indicates an increase in the influence of meteoric water on the hydrologic budget under wet conditions, possibly driven by a strengthened Aleutian Low atmospheric pressure cell. A shift to lower δ13Cmarl and δ18Omarl values at ~11.5 ka is interpreted as an increase in the proportion of groundwater relative to meteoric water in the lake. Beginning around 9 ka, the proportion of meteoric water input continued to increase, the surrounding coniferous forest was established, and by 8 ka, CaCO3 accumulation ended. Our results elucidate the environmental conditions under which marl was deposited during the Lateglacial and early Holocene in this part of Alaska, and demonstrate how a variety of synoptic‐ and local‐scale climatic variables can converge to influence sedimentation in a groundwater‐fed lake.