Three-dimensional density-dependent flow and transport modeling of the Floridan aquifer system, USA shows that current chloride concentrations are not in equilibrium with current sea level and, second, that the geometric configuration of the aquifer has a significant effect on system responses. The modeling shows that hydraulic head equilibrates first, followed by temperatures, and then by chloride concentrations. The model was constructed using a modified version of SUTRA capable of simulating multi-species heat and solute transport, and was compared to pre-development conditions using hydraulic heads, chloride concentrations, and temperatures from 315 observation wells. Three hypothetical, sinusoidal sea-level changes occurring over 100,000 years were used to evaluate how the simulated aquifer responds to sea-level changes. Model results show that hydraulic head responses lag behind sea-level changes only where the Miocene Hawthorn confining unit is thick and represents a significant restriction to flow. Temperatures equilibrate quickly except where the Hawthorn confining unit is thick and the duration of the sea-level event is long (exceeding 30,000 years). Response times for chloride concentrations to equilibrate are shortest near the coastline and where the aquifer is unconfined; in contrast, chloride concentrations do not change significantly over the 100,000-year simulation period where the Hawthorn confining unit is thick.