This study evaluates how alteration of geosynthetic clay liners (GCLs) affects the hydraulic behaviour of a composite liner when the geomembrane presenting a hole is overlying a GCL. Interface transmissivity experiments were performed on GCL specimens that were exhumed from field sites. The results reveal different trends in the flow rates, which decrease differently to their steady state values. The steady state flow rates obtained and the calculated interface transmissivities are of the same order of magnitude as results obtained with a virgin GCL. The transient flow rate results are discussed in relation with the GCLs parameters. Based on these results, a new equation is derived that links interface transmissivity to the hydraulic conductivity of GCLs that have been altered by the environment. Considering large transient flow rates in calculations result in a greater leakage volume penetrating the liner when compared to calculations of infiltrated volumes considering only steady state leakage volume for a period of time of 1, 10 or 30 years. From a practical point of view, this suggests the introduction of a factor of safety of 1.67 when calculating the flow rate in composite liners in order to take into account the alteration by the environment of GCLs.