The spatial variability of layer-scale hydrogeologic properties of the unsaturated zone (UZ) at Yucca Mountain, Nevada, is investigated using inverse modeling. The thick UZ is grouped into five hydrostratigraphic units and further into 35 hydrogeologic layers. For each layer, lateral variability is represented by the variations in calibrated values of layer-scale properties at different individual deep boreholes. In the calibration model, matrix and fracture properties are calibrated for the one-dimensional vertical column at each individual borehole using the ITOUGH2 code. The objective function is the summation of the weighted misfits between the ambient unsaturated flow (represented by measured state variables: water saturation, water potential, and pneumatic pressure) and the simulated one in the one-dimensional flow system.