The characterization of protective coatings applied on natural stones is often a complex task due to the difficulty of identifying and quantifying the various factors contributing to the overall behaviour of the coating-stone system. In particular, linking information about the coating-stone interaction to macroscopic effects in terms of physical behaviour of treated stones can be especially arduous owing to the inherent structural complexity of stone substrates. Electrokinetic analysis based on streaming current measurements, having already proved the ability to sense even minor changes in the chemical composition of different materials surfaces upon treatment, may provide useful insights in view of better understanding the extent of stone surface modification. In particular, involving the interaction of stones with a water-based solution, the streaming current technique could extend the characterization of stone surface to the outermost part of the pore network, which is part of every treatment-induced modification of surface properties. In this work, the effectiveness of streaming current measurements as analytical tool for the characterization of coatings applied on natural stones is assessed by considering different lithotypes and coatings and trying to correlate the results of electrokinetic analysis with the physical behaviour of treated stones, with specific regard to wettability and capillary water absorption.