The regional Floridan aquifer system (FAS) extends from the submerged carbonate platform of the Atlantic Ocean, Gulf of Mexico, and Straits of Florida in the southeastern United States (US), throughout Florida and the coastal plain of Alabama, Georgia, and South Carolina. This carbonate aquifer system is characterized by bedding planes, fractures, dissolution cavities, and other karst features that result in preferential flow of ground water, particularly in response to anthropogenic perturbations such as groundwater withdrawals and aquifer injections. The FAS was divided into six sub-regions for groundwater-modeling purposes in 1989, with results concluding that breaches of those groundwater divides had occurred and those breaches were attributed to large withdrawals of ground water in the US southeastern coastal plain. Those results suggest the model did not elucidate preferential flow conditions through fractures and other karst conduits. We hypothesized that incorporating fractures and sinkholes into groundwater models could improve results and predict adverse impacts to environmentally sensitive areas. We analyzed extensive fracture networks and sinkholes previously mapped throughout Florida and in Dougherty County, Georgia. Some of those fractures extend from one sub-region into an adjacent sub-region of the FAS and may be facilitating the breaching of groundwater divides described in the 1989 groundwater model for this regional aquifer system. The greater total fractures and fracture density in Dougherty County (1,225 and 141.3/100 km2, respectively) compared to 21 north-Florida counties (10-91fractures per county and 0.6-3.8/100 km2, respectively) presumably is due to the scale of fracture mapping and shorter mean lengths of mapped fractures in Dougherty County (1.2 km), compared to north Florida counties (26-118 km), rather than to orders of magnitude increases in fracture densities in that part of the FAS. The number of sinkholes identified in Dougherty County in a recent, unrelated project using 2011 Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) images, was approximately an order of magnitude greater than the number of sinkholes mapped in analog form in that county and published in 1986. Extension of the dense network of those fractures that occurred within the boundaries of a Priority Amphibian and Reptile Conservation Area (PARCA) that encompassed Dougherty County covered the Elmodel Wildlife Management Area (WMA) and ASR demonstration well in Baker County, Georgia. Those extensions also passed through numerous agricultural areas with center-pivot irrigation wells in southwest Georgia; intersected other Georgia PARCAs near the Florida-Georgia state line; and clumped in two areas of dense sinkhole clusters in northwest Florida. No determination has been made regarding the contributions of pirated water from the Apalachicola-Chattahoochee-Flint (ACF) River Basins and Wakulla Springshed from the magnitude and extent of agricultural, municipal, and industrial groundwater withdrawals in Georgia’s coastal plain, that exceed groundwater withdrawals in Florida for that area of the FAS, to the increase in sinkholes in Dougherty County and the dense clusters of sinkholes in northwest Florida, via preferential flow through fractures. Similarly, the survival and recovery of at least 24 animal species in Georgia that are either federally listed or high-priority state species may be jeopardized by adverse direct, indirect, and cumulative impacts from preferential flow through fractures, sinkholes, and other karst conduits in response to aquifer injections and withdrawals that have not been evaluated. Currently no regional groundwater model has been constructed to evaluate such preferential groundwater flow in the FAS. A model incorporating preferential flow via mapped fractures and sinkholes is essential to determine the magnitude and extent of environmental impacts from ASR wells and other supply and disposal wells in this regional aquifer system, such as pirated water from the ACF and other river basins, alterations in submarine groundwater discharge to Apalachicola Bay and other coastal areas, saltwater intrusion, upconing of saline ground water and resulting impacts to federally endangered and threatened species and high-priority state species.