Sea‐level rise and changes in precipitation patterns may contribute to the occurrence and affect the rate of saltwater contamination in the Hilton Head Island, South Carolina area. To address the effects of climate change on saltwater intrusion, a threedimensional, finite‐element, variable‐density, solute‐transport model was developed to simulate different rates of sea‐level rise and variation in onshore freshwater recharge. Model simulation showed that the greatest effect on the existing saltwater plume occurred from reducing recharge, suggesting recharge may be a more important consideration in saltwater intrusion management than estimated rates of sea‐level rise. Saltwater intrusion management would benefit from improved constraints on recharge rates by using model‐independent, local precipitation and evapotranspiration data, and improving estimates of confining unit hydraulic properties.