The surface ecology of small ocean islands is directly linked to subsurface fresh water resources, which exist in the form of soil water and fresh groundwater lenses. The management of threaten plant species such as the tree Pisonia grandis needs to consider the spatial and temporal dynamics of groundwater lenses, particularly in a time of climate change. The Palmyra Atoll National Wildlife Refuge is located in the Central Pacific Ocean in the Northern Line Islands. The atoll consists of a series of small, predominantly forested islets surrounding central lagoon areas, with a maximum mean elevation above sea level for all of the islets less than ~2 m. The atoll is home to some of the few remaining stands of native Pisonia in the Pacific Ocean, yet the distribution of fresh groundwater was not previously characterized. Here, we present electromagnetic induction data collected in 2008 and 2016 during wetter and dryer periods, respectively, as driven by El Niño /La Niña climate cycles. This data release contains raw and processed geophysical data from hand-carried frequency domain (FDEM) data collected with the GEM-2 instrument (Geophex, Ltd.) at approximately 0.75 m off the ground in vertical magnetic dipole mode (2008 and 2016). Data were collected along several transects on the main Cooper-Meng island and on the smaller Eastern Island. The thickness of the fresh groundwater lens under Cooper-Meng was greater than the depth of investigation of the FDEM tool. Therefore, to substantially enhance the investigation depth along the Cooper-Meng island runway transect, a transient electromagnetic system (TEM), known as the WalkTEM (Guideline Geo, Inc.), was utilized in 2016. FDEM data were collected along continuous, georeferenced walking lines while TEM data were collected at fixed points setup with 40 or 20 m transmitter loop sizes. For the latter, 20 m loops were used in proximity to the shoreline where higher spatial resolution was desired. To support the geophysical data interpretation and to monitor the fresh/saline groundwater interface at high resolution over time, a series of shallow monitoring wells were installed in 2013. A subset of monitoring wells were instrumented within the screened interval with temperature, specific conductance (SpC), and water pressure (non-vented) loggers (Solinst Levelogger Model 3001, Solinst Ltd.) recording at 3-hr intervals for varied lengths of time. Also, in April 2017, a temperature and SpC logger (Model CS547A-L, Campbell Scientific, Inc.) and vented water pressure logger (Model CS451, Campbell Scientific, Inc.) were deployed in MW1 and connected to the adjacent weather station data logger (Campbell Scientific CR1000), and data were collected at 15 min intervals until September 2019. Further details regarding monitoring well locations are listed within the ‘ReadMe’ file of the related raw data zipper folder.