The Little River, an ephemeral stream that drains a watershed of approximately 88 km2 in northern Florida, disappears into a series of sinkholes along the Cody Scarp and flows directly into the carbonate Upper Floridan aquifer, the source of water supply in northern Florida. The changes in the geochemistry of ground water caused by a major recharge pulse from the sinking stream were investigated using chemical and isotopic tracers and mass-balance modeling techniques. Nine monitoring wells were installed open to the uppermost part of the aquifer in areas near the sinks where numerous subterranean karst solution features were identified using ground penetrating radar. During high-flow conditions in the Little River, the chemistry of water in some of the monitoring wells changed, reflecting the mixing of river water with ground water. Rapid recharge of river water into some parts of the aquifer during high-flow conditions was indicated by enriched values of delta 18O and delta deuterium (-1.67 to -3.17 per mil and -9.2 to -15.6 per mil, respectively), elevated concentrations of tannic acid, higher (more radiogenic) 87Sr/86Sr ratios, and lower concentrations of 222Rn, silica, and alkalinity compared to low-flow conditions. The proportion of river water that mixed with ground water ranged from 0.10 to 0.67 based on binary mixing models using the tracers 18O, deuterium, tannic acid, silica, 222Rn, and 87Sr/86Sr. On the basis of mass-balance modeling during steady-state flow conditions, the dominant processes controlling carbon cycling in ground water are the dissolution of calcite and dolomite in aquifer material, and aerobic degradation of organic matter.The Little River of northern Florida disappears into a series of sinkholes along the Cody Scarp and flows directly into the carbonate Upper Floridan aquifer. The changes in the geochemistry of ground water caused by a major recharge pulse from the sinking stream were investigated using chemical and isotopic tracers and mass-balance modeling techniques. Nine monitoring wells were installed open to the uppermost part of the aquifer. During high-flow conditions in the Little River, the chemistry of water in some of the monitoring wells changed, reflecting the mixing of river water with ground water. Based on mass-balance modeling during steady-state flow conditions, it was found that the dominant processes controlling carbon cycling in ground water are the dissolution of calcite and dolomite in aquifer material, and aerobic degradation of organic matter.