The study of charge transport through increasingly complex small molecules will benefit from a detailed understanding of how contaminants from the environment affect molecular conduction. This should provide a clearer picture of the electronic characteristics of molecules by eliminating interference from adsorbed species. Here we use magnetically assembled microsphere junctions incorporating thiol monolayers to provide insight into changing electron transport characteristics resulting from exposure to air. Using this technique, current-voltage analysis and inelastic electron tunnelling spectroscopy (IETS) demonstrate that the primary interaction affecting molecular conduction is rapid hydration at the gold-sulphur contacts. We use IETS to present evidence for changing mechanisms of charge transport as a result of this interaction. The detrimental effects on molecular conduction discussed here are important for understanding electron transport through gold-thiol molecular junctions once exposed to atmospheric conditions.