This paper investigates the localized 3D imaging of equatorial ionospheric depletions and mesoscale traveling ionospheric disturbances (MS-TIDs) with a dense ground-based GPS receiver array. A tomographic forward model is presented using dual-frequency GPS measurements from receivers in the Japanese GPS Earth Observation Network (GEONET). The application of inversion techniques to the discrete observation matrix allows a 3D electron density volume to be reconstructed from the GPS total electron content (TEC) measurements. Because the inverse problem is ill-posed and ill-conditioned, regularization functionals are used to constrain the solution in the presence of noise. To capture the abrupt height and density variations of the structures, a technique using nonconvex penalty constraints is proposed. The reconstructions have 40 to 50-km horizontal and 30-km vertical resolution. Time series of reconstructed images show the evolution and movement of ionospheric structures through the reconstruction region. The results are analyzed and compared with independent ionosonde measurements and vertical TEC (VTEC) maps constructed from the observed GPS data.