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The Pearl Harbor aquifer, an important ground‐water resource for southern Oahu, Hawaii, contains an enormous fresh‐water lens, up to 300 m (1,000 ft) thick, floating above saline water. The upper boundary of the fresh‐water lens is confined near the coast and phreatic inland, whereas its lower boundary is not confined. A finite‐difference flow model was used to simulate the Pearl Harbor aquifer system. The location of the fresh‐water/salt‐water interface, which constitutes the lower boundary of the flow system model, was estimated by Hubbert's formula. Known geohydrologic boundaries and aquifer parameters were also simulated. First, formation of the lens by filling the aquifer with fresh water from natural recharge was simulated to reconstruct the initial conditions before exploitation of the lens and to partially calibrate the model against the hydraulic‐head distribution in 1879. The model then was calibrated fully by simulating the lens’reponse to actual historical pumping patterns covering a time span of 100 years (1880 to 1980). Simulated heads compared favorably with the observed heads over time and space. The calibrated flow model may serve as a useful tool in the management of the Pearl Harbor aquifer.