Mangrove ecosystems rely on seawater, rain-derived flow, and groundwater for hydrologic sustenance, flushing, and inflow of nutrients and sediments. The relative contribution of these source waters and their variability through time and space can provide key information concerning the hydrologic function of ecosystems. We used hydrologic tracers to partition source waters and trace their movements in the Enipoas stream, a river-dominated mangrove ecosystem on the island of Pohnpei, Federated States of Micronesia (FSM) and in the Yela watershed, an interior mangrove ecosystem on the island of Kosrae, FSM. The Enipoas site was characterized as a salt wedge estuary whose source water contributions alternated between predominantly seawater and rain-derived flow, depending on the tide. The source waters in the interior Yela site were also predominantly seawater and rain-derived flow, however the relative contribution of each was much more stable. The mean groundwater contribution was 5% (SD = 5.5) for the Enipoas site and 20% (SD = 11.0) for the Yela site. Although a small contributor to flow, groundwater was a steady source of freshwater for both systems. Hydrologic linkages between mangroves and adjacent ecosystems were demonstrated by the temporal and spatial distribution of source waters. The 0.8 km Enipoas estuary, with its highly dynamic bi-directional flows, transported source waters along a hydrologic continuum comprised of coral reef, mangroves, and palm forest. In the interior mangroves of the Yela watershed, the presence of rain-derived flow and groundwater demonstrated a hydraulic connection between the mangroves and an upstream freshwater swamp. Interior mangroves with such linkages avoid stresses such as desiccation and heightened salinity, and thus are more productive than those with little or no freshwater flows.