The potential effects of global climate change on coastal ecosystems have attracted considerable attention, but the impacts of shorter-term climate perturbations such as ENSO (El Niño-Southern Oscillation) are lesser known. In this study, we determined the effects of the 1997–1998 ENSO-related drought on the hydrology and salinity of a Micronesian mangrove ecosystem and an adjacent freshwater swamp. A network of 9 piezometer clusters installed at the study site served as sampling points for continuous and manual measurements of salinity and water level. During the drought period from January through April 1998, mean water table levels in the mangroves and freshwater swamp were approximately 12 and 54 cm lower, respectively, than during May through December when precipitation returned to near normal levels. At the peak of the drought (February 1998), the most dramatic result was a reversal in groundwater flow that sent groundwater from the mangroves upstream toward the freshwater swamp. Flow nets constructed for this period and immediately after illustrate the strong hydrological linkage between the two systems. This linkage was also illustrated by measurements of groundwater salinity in the piezometer network. Ninety-six percent of the salinity measurements taken in the mangroves during the study were at least 10‰ less than the salinity of sea water, indicating that the mangroves were consistently receiving freshwater flows. An analysis of variance of groundwater salinity measurements during and after the drought showed that salinity levels in the 0.5 and 1.0 m depth piezometers were greater during than after the drought. In a comparison of salinity values in 0.5-m wells during low tide, mean salinity was approximately twice as high during the drought than after (14.7‰ versus 6.2‰, respectively). This study demonstrates that short-term climate perturbations such as ENSO can disrupt important coastal processes. Over repeated drought cycles, such perturbations have the potential to affect the structure and function of mangrove forests and upstream ecosystems.