This paper presents an analytical solution developed to estimate probabilities of “failure” or advective flux “exceedance” for the case of a spatially variable geosynthetic clay liner (GCL) situated over a spatially variable compacted soil liner (CSL). The risk of utilizing such a liner system is assessed relative to a regulatory compacted clay-based soil liner. The analytical solution developed is validated over a range of parameters against random field simulation using the Local Average Subdivision method, and the analytical solution is shown to be in good agreement with simulation. The analytical solution is then used to examine the “probability of exceedance” for a spatially variable GCL and CSL combined liner system. It is shown that the use of a GCL can potentially result in a low probability of exceedance when used with a spatially varying, high hydraulic conductivity CSL. The risk of exceedance generally decreases as the hydraulic conductivity of the CSL decreases. An example problem is presented to demonstrate the capabilities of the analytical solution.