Stable isotopes of hydrogen and oxygen were used to trace the sources of recharge from sinking streams to wells and springs several kilometers downgradient in the karst Madison aquifer near Rapid City, South Dakota. Temporal sampling of streamflow above the swallets identified a distinct isotopic signature that was used to define the spatial dimensions of recharge to the aquifer. When more than one sinking stream was determined to be recharging a well or spring, the proportions were approximated using a two-component mixing model. From the isotopic analysis, it is possible to link sinking stream recharge to individual wells or springs in the Rapid City area and illustrate there is significant lateral movement of ground water across surface drainage basins. These results emphasize that well-head protection strategies developed for carbonate aquifers that provide industrial and municipal water supplies need to consider lateral movement of ground-water flow from adjacent surface drainage basins.