Freshwater lenses underlying small ocean islands exhibit spatial variability and temporal fluctuations in volume, influencing ecologic management. For example, The Palmyra Atoll National Wildlife Refuge harbors one of the few surviving native stands of Pisonia grandis in the central Pacific Ocean, yet these trees face pressure from groundwater salinization, with little basic groundwater data to guide decision making. Adding to natural complexity, the geology of Palmyra was heavily altered by dredge and fill activities. Our study based at this atoll combines geophysical and hydrological field measurements from 2008 to 2019 with groundwater modeling to study the drivers of observed freshwater lens dynamics. Electromagnetic induction (EMI) field data were collected on the main atoll islands over repeat transects in 2008 following ‘strong’ La Niña conditions (wet) and in 2016 during ‘very strong’ El Niño conditions (dry). Shallow monitoring wells were installed adjacent to the geophysical transects in 2013 and screened within the fresh/saline groundwater transition zone. Temporal EMI and monitoring well data showed a strong contraction of the freshwater lens in response to El Niño conditions, and indicated a thicker lens toward the ocean side, an opposite spatial pattern to that observed for many other Pacific islands. On an outer islet where a stand of mature Pisonia trees exist, EMI surveys revealed only a thin (<3 m from land surface) layer of brackish groundwater during El Niño. Numerical groundwater simulations were performed for a range of permeability distributions and climate conditions at Palmyra. Results revealed that the observed atypical lens asymmetry is likely due to more efficient submarine groundwater discharge on the lagoon side as a result of lagoon dredging and filling with high-permeability material. Simulations also predict large decreases (40%) in freshwater lens volume during dry cycles and highlight threats to the Pisonia trees, yielding insight for atoll ecosystem management worldwide.