Many freshwater lakes are groundwater flow-through systems. Although lakes commonly are considered to be sinks for nitrogen inputs, relatively little is known about carbon and nitrogen export from lakes to groundwater. The current study focused on lake-bottom biogeochemical processes accompanying the transport of nitrogen, dissolved oxygen (O₂), and dissolved organic carbon (DOC) during lake-water recharge from a groundwater flow-through lake. Lake-water and porewater (15–100 cm below lakebed) samples were collected along transects within the lake downwelling zone. Infiltrating porewater O₂ and DOC concentrations decreased with depth while nitrate (NO₃⁻) concentrations increased, indicating nitrification of organic matter within the profiles. The depth of NO₃⁻ production and transport was seasonally dependent. In winter, NO₃⁻ and O₂ were exported beyond 100-cm depth; whereas in summer, shallow nitrification zones were underlain by deeper NO₃⁻ reduction zones, and diel patterns of O₂ and NO₃⁻ penetration depths were observed. Microbial community compositions and stable isotope profiles (δ¹⁵N[NO₃⁻], δ¹⁸O[NO₃⁻], δ¹⁸O[O₂]) were consistent with apparent C–N–O reaction stoichiometries indicating O₂ reduction and nitrification in shallower porewater, followed by varying NO₃⁻ reduction at depth. Maximum porewater NO₃⁻ concentrations (∼10–20 μM) were limited by infiltrating O₂ concentrations and C/N ratios of reacting organic matter. Lake-water level variations caused changes in shoreline position and porewater velocities, while variations in lake-water temperature, DOC, and O₂ contributed to changes in reaction rates and depth of O₂ and NO₃⁻ penetration into the lakebed. The quality of groundwater recharged by lake water reflected temporally and spatially varying physical and biogeochemical processes in the sediment porewater.