This work presents the methodological approach followed for the study of the interaction of natural stone monuments with the local microclimate (exposure to RH, temperature alterations, wind, marine aerosol). This was implemented with the documentation of the associated weathering phenomena and the study of historic climate data of the area. The paper is focused on the main weathering mechanisms of the marly limestone at the Hellenistic theater of Zea in Piraeus, Greece. Based on the weathering phenomena identified, the development of the appropriate mitigation strategy was based on the physical, chemical and mechanical characterization of the natural stones, along with the evaluation of different conservation treatments, considering the characteristics of the coastal environment. Considering the mineralogy of marly limestones, silane-based materials were selected for providing both consolidation and water repellency effects. The evaluation of the conservation treatments was based on the modification of microstructural and water-related properties of natural stone samples, along with their consequent effect on their durability against accelerated aging tests. The results indicated that the design of migration actions proved to be multivariable parameter, depending on the intrinsic stone properties, the environmental parameters and the conservation efficacy of the treatments.