The objective of this study is to evaluate the effect of the geomembrane/geotextile interface on the seismic response of small-to-moderate height structures. Three building models with first-mode natural frequencies changing between 2–4 Hz (representing two, three and four storey structures) were tested with and without the addition of geomembrane/geotextile interface using the shaking table test setup by employing harmonic and modified/scaled ground motions. Experimental results showed that the geomembrane/geotextile interface significantly reduced the floor accelerations, especially at moderate-to-high ground shaking levels. The interaction between the first-mode natural frequency of the model and the predominant frequency of the input motion is significant, and the interface is most effective when these two frequencies are close to each other. This effect is more clearly seen when the harmonic motions are employed during the tests compared to the modified/scaled ground motions. The results of the tests with modified/scaled ground motions were used to evaluate the efficiency of the composite liner system in reducing the spectral accelerations in the frequency domain. The results presented here document that the geomembrane/geotextile interface reduces the floor accelerations in a certain frequency range and underline the potential of this interface to be used as a base isolation material.