Coastal forested hummocks support clusters of trees in the saltwater–freshwater transition zone. To examine how hummocks support trees in mesohaline sites that are beyond physiological limits of the trees, we used salinity and stable isotopes (²H and ¹⁸O) of water as tracers to understand water fluxes in hummocks and uptake by baldcypress (Taxodium distichum (L.) Rich.), which is the most abundant tree species in coastal freshwater forests of the southeastern U.S. Hummocks were always partially submerged and were completely submerged 1 to 8% of the time during the two studied growing seasons, in association with high water in the estuary. Salinity, δ¹⁸O, and δ²H varied more in the shallow open water than in groundwater. Surface water and shallow groundwater were similar to throughfall in isotopic composition, which suggested dominance by rainfall. Salinity of groundwater in hummocks increased with depth, was higher than in swales, and fluctuated little over time. Isotopic composition of xylem water in baldcypress was similar to the vadose zone and unlike other measured sources, indicating that trees preferentially use unsaturated hummock tops as refugia from higher salinity and saturated soil in swales and the lower portions of hummocks. Sustained upward gradients of salinity from groundwater to surface water and vadose water, and low variation in groundwater salinity and isotopic composition, suggested long residence time, limited exchange with surface water, and that the shallow subsurface of hummocks is characterized by episodic salinization and slow dilution.