Hydraulic parameters of the vadose zone at a spatial resolution typically larger than 1 km2 are a key input for land–atmosphere feedback schemes in soil–vegetation–atmosphere transfer (SVAT) models. Previous studies investigated the significance of first- and second-order moments of soil hydraulic parameters on “effective” parameter estimation in heterogeneous soils at the landscape or remote-sensing footprint/pixel scale. In this study, we examined the impact of the skewness (third-order moment) of hydraulic parameter distributions on “effective” soil hydraulic parameter averaging schemes for steady-state vertical flow in heterogeneous soils in a flat landscape. The effective soil hydraulic parameter of the heterogeneous soil formation is obtained by conceptualizing the soil as an equivalent homogeneous medium. The averaging scheme requires that the effective homogeneous soil will discharge the same ensemble moisture flux across the soil surface. Using three widely used unsaturated hydraulic conductivity functions and various types of probability distribution functions to represent spatial variability for the nonlinear shape factor in the hydraulic conductivity function, we derive the effective parameter values. Numerical and field experimental results show that distribution skewness is also important in determining the upscaled effective parameters in addition to the mean and variance. Negative skewness enhances heterogeneity effects, which make the “effective” α parameter deviate more significantly from the arithmetic mean. In the case of negative skewness, a few small α values make the heterogeneous soil more permeable (with larger flux), which hence causes the “effective” heterogeneous system to deviate more from the homogeneous formation with arithmetic mean parameters.