Three-dimensional porosity and permeability were modeled in an Ellenburger carbonate reservoir analog from 2D crosshole and 3D surface survey ground-penetrating radar (GPR) data. Two-dimensional GPR crosshole velocity tomography, 3D migration of the GPR surface data, and porosity and permeability calibration to GPR attributes results in 3D porosity and permeability predictions that provide a consistent model of the paleocave structures and facies distributions. Picking the maximum instantaneous amplitude of the direct arrival wavelet for velocity tomography reduces uncertainties caused by a low signal-to-noise ratio, uncorrelated noise, and the interference between reflections and critical refractions at the earth/air interface. The GPR velocity is anisotropic with an average vertical to horizontal velocity ratio of 0.93, which is attributed to the dominance of the relatively horizontal orientation of the maximum porosity and permeability. Porosity and permeability trends are influenced by regional northeast-southwest and northwest-southeast striking conjugate fractures associated with the Pennsylvanian Ouachita orogeny and breccia facies generated by three episodes of burial and the resulting paleocave collapses. At depths from the present surface, large brecciated dolomite and limestone blocks have low porosity and low permeability. Between a depth of and irregular fracture orientations and distributions associated with collapse breccias have a higher average porosity and permeability. A deeper zone ( to in depth), has intermediate permeability and porosity. Porosity and permeability could not be calibrated in open voids. Thus, the predictions are applicable to the core-scale to which they were calibrated, but are lower bounds for the whole volume, which contains breccias, karst, and fractures that increase both porosity and permeability at larger scales.