Atmospheric pollutants may cause damage to monuments and historical buildings. Besides air contaminants, soluble salts are also responsible for stone deterioration and decay in outdoor and indoor monuments. The problem of how to conserve works of arts thus requires a deep knowledge of contaminants' concentration and distribution inside buildings. In this work, water-soluble ions inside St. Mark's Basilica in Venice were studied, with the aim of understanding their principal source and distribution inside the building. With the aid of Fourier transform infrared spectroscopy and scanning electron microscopy analysis, the interaction between ions and surface's material was also investigated. Ion chromatographic analysis of depositions highlighted a large amount of "deteriorating agents" such as sulphates and chlorides. A possible source in the innermost area of the basilica has been found for formates and nitrates. On the contrary, a decrease of chloride, from the entrance to the innermost area, has been found, which indicates that the source is outside the building. It is emphasized that different contaminants behave differently on different material, and the effect of pollution inside churches and monuments is not easy to predict. Wood and brick seem to react differently than stone and mortar to the damaging action of salts and pollutants. The present work should be considered a useful tool for the future preservation of St. Mark's Basilica in Venice.