Securing water pumping is a considerable challenge in small, flat atoll islands where rivers and lakes do not develop. Excess pumping due to water shortages during severe droughts has caused up-coning in the fresh groundwater lens (FGL). Since FGL may not recover from up-coning, very few researchers have attempted to clarify the three-dimensional pumping effect on the saltwater–freshwater interface of FGL. The purpose of this research is twofold: (1) to clarify the three-dimensional distributed pumping effect on the FGL flow in Laura Island, and (2) to suggest the up-coning mitigation method for the FGL on Laura Island (Laura Lens). The Republic of the Marshall Islands (RMI), a region of increasing population growth that could burden Laura Lens, was selected as the research site. First, we collected various on-site information and analyzed the hydrological data. We observed a correlation between the rainfall data recorded on Laura Island and Majuro Atoll. Subsequently, numerical simulation using the SEAWAT model clarified the movement of Laura Lens during water pumping in a drought situation. As a result, we could also report the optimum period and the volume of water pumping for the Laura Lens. In conclusion, findings for RMI can facilitate sustainable management and conservation of FGL on atoll islands to reduce up-coning by realizing distributed pumping.