Hydrogeologic data and water-chemistry analyses indicate that Lake Seminole leaks into the Upper Floridan aquifer near Jim Woodruff Lock and Dam, southwestern Georgia and northwestern Florida, and that ground water enters Lake Seminole along upstream reaches of the lake’s four impoundment arms (Chattahoochee and Flint Rivers, Spring Creek, and Fishpond Drain). Written accounts by U.S. Army Corps of Engineers geologists during dam construction in the late 1940s and early 1950s, and construction-era photographs, document karst-solution features in the limestone that comprise the lake bottom and foundation rock to the dam, and confirm the hydraulic connection of the lake and aquifer. More than 250 karst features having the potential to connect the lake and aquifer were identified from preimpoundment aerial photographs taken during construction. An interactive map containing a photomosaic of 53 photographic negatives was orthorectfied to digital images of 1:24,000-scale topographic maps to aid in identifying karst features that function or have the potential to function as locations of water exchange between Lake Seminole and the Upper Floridan aquifer. Some identified karst features coincide with locations of mapped springs, spring runs, and depressions that are consistent with sinkholes and sinkhole ponds.

Hydrographic surveys using a multibeam echosounder (sonar) with sidescan sonar identified sinkholes in the lake bottom along the western lakeshore and in front of the dam. Dye-tracing experiments indicate that lake water enters these sinkholes and is transported through the Upper Floridan aquifer around the west side of the dam at velocities of about 500 feet per hour to locations where water "boils up" on land (at Polk Lake Spring) and in the channel bottom of the Apalachicola River (at the "River Boil"). Water discharging from Polk Lake Spring joins flow from a spring-fed ground-water discharge zone located downstream of the dam; the combined flow disappears into a sinkhole located on the western floodplain of the river and is transmitted through the Upper Floridan aquifer, eventually discharging to the Apalachicola River at the River Boil. Acoustic Doppler current profiling yielded flow estimates from the River Boil in the range from about 140 to 220 cubic feet per second, which represents from about 1 to 3 percent of the average daily flow in the river. Binary mixing-model analysis using naturally occurring isotopes of oxygen and hydrogen (oxygen-18 and deuterium) indicates that discharge from the River Boil consists of a 13-to-1 ratio of lake water to ground water and that other sources of lake leakage and discharge to the boil probably exist.

Analyses of major ions, nutrients, radon-222, and stable isotopes of hydrogen and oxygen contained in water samples collected from 29 wells, 7 lake locations, and 5 springs in the Lake Seminole area during 2000 indicate distinct chemical signatures for ground water and surface water. Ground-water samples contained higher concentrations of calcium and magnesium, and higher alkalinity and specific conductance than surface-water samples, which contained relatively high concentrations of total organic carbon and sulfate. Solute and isotopic tracers indicate that, from May to October 2000, springflow exhibited more ground-water qualities (high specific conductance, low dissolved oxygen, and low temperature) than surface water; however, the ratio of ground water to surface water of the springs was difficult to quantify from November to April because of reduced springflow and rapid mixing of springflow and lake water during sampling. The saturation index of calcite in surface-water samples indicates that while surface water is predominately undersaturated with regard to calcite year-round, a higher potential for dissolution of the limestone matrix exists from late fall through early spring than during summer.

The relatively short residence time (5–7 hours) and rapid flow velocity (nearly 500 feet per hour) of lake water leaking into the Upper Floridan aquifer and exiting at the River Boil in the Apalachicola River implies that calcite-undersaturated water is in constant contact with the limestone, increasing the potential for limestone dissolution and enlargement of flow pathways by erosion. A relatively low potential exists, however, for limestone dissolution to cause sudden sinkhole collapse followed by catastrophic lake drainage because ground-water levels close to the lake, except near the dam, are nearly the same as lake stage, resulting in low vertical and lateral hydraulic gradients and low flow between the lake and aquifer. An increased potential for lake leakage and sinkhole formation and collapse exists near some in-lake springs during colder months of the year, as density differences and the hydraulic potential between lake water and ground water establish the conditions for calcite-undersaturated lake water to enter nonflowing springs and contact limestone.