Exchanges of water between the Upper Floridan aquifer and the Lower Suwannee River were evaluated using historic and current hydrologic data from the Lower Suwannee River Basin and adjacent areas that contribute groundwater flow to the lowest 76 miles of the Suwannee River and the lowest 28 miles of the Santa Fe River. These and other data were also used to develop a computer model that simulated the movement of water in the aquifer and river, and surface-and groundwater exchanges between these systems over a range of hydrologic conditions and a set of hypothetical water-use scenarios. Long-term data indicate that at least 15 percent of the average annual flow in the Suwannee River near Wilcox (at river mile 36) is derived from groundwater discharge to the Lower Suwannee and Lower Santa Fe Rivers. Model simulations of groundwater flow to this reach during water years 1998 and 1999 were similar to these model-independent estimates and indicated that groundwater discharge accounted for about 12 percent of the flow in the Lower Suwannee River during this time period. The simulated average groundwater discharge to the Lower Suwannee River downstream from the mouth of the Santa Fe River was about 2,000 cubic feet per second during water years 1998 and 1999. Simulated monthly average groundwater discharge rates to this reach ranged from about 1,500 to 3,200 cubic feet per second. These temporal variations in groundwater discharge were associated with climatic phenomena, including periods of strong influence by El Niñoassociated flooding, and La Niña-associated drought. These variations showed a relatively consistent pattern in which the lowest rates of groundwater inflow occurred during periods of peak flood levels (when river levels rose faster than groundwater levels) and after periods of extended droughts (when groundwater storage was depleted). Conversely, the highest rates of groundwater inflow typically occurred during periods of receding levels that followed peak river levels.