To mitigate the impact on cultural heritage structures damaged by water, it is crucial to implement conservation-compatible and non-invasive strategies. These methods should consider the site’s specific conditions as well as the material properties and characteristics of the artworks associated with the structure. Due to the presence of water causing damage to the under level site of Mensa Ponderaria in Tivoli (Rome-Italy), before proceeding with conservative and restoration efforts, demonstration studies were carried out to evaluate suitable heritage treatment strategies for drying the site. The building, discovered in 1883 dated to the first century AD, served as a public weighhouse, which was identified by the presence of two marble mensae with concave cavities for official weights. A structure in close proximity, unearthed in 1920, is presumed to have been dedicated to the imperial cult (Augusteum). To preserve the original opus reticulatum interior of the wall treated, it was necessary to observe specific temperature constraints throughout the drying procedure. In this context, direct volumetric heating methods utilizing electromagnetic waves in the microwave frequency range were employed through a two-step procedure (treat and measure). Specifically, a 2.45 GHz, 1.5 kW antenna equipped with a focalization horn was utilized, defining duty cycle and duration to ensure proper evaporation without risking overheating and measuring the amount of removed water. This approach highlighted the effectiveness of microwave techniques in treating water-damaged buildings while safeguarding their original features. Comprehensive studies included on-site heating tests and experiments on masonry specimens representative of heritage materials, confirming the successful removal of moisture using these techniques. Subsequent restoration efforts focused on the frescoes, flooring, and statue housed in the Augusteum.