The present study investigated the correlation between the degradation processes of cultural heritage and the environmental parameters of the semi-confined site that houses it. The latter is a semi-underground room (nymphaeum) found in the Archaeological Park of Baia (Italy) dating back to the third century; it is decorated with marine motifs and painted with frescos techniques from the same period. Relative humidity and temperature were hourly registered, and the collected data were used to derive daily and annual profiles. The effects of microclimate induced degradation were investigated employing various techniques, such as Ion Chromatography for the chemical characterisation of deposits, and Thermography, for the individuation of biological layers. The data obtained showed that the underground environment, partially submerged by rising brackish water, was affected by the presence of biodeteriogens, whose distribution and growth is strongly favoured, above all, by the environmental parameters and by the substrate characteristics. All the data were then cross-referenced to obtain a complete knowledge of the conservation frameworks of the environments, essential to identify the most compatible and effective restoration methodologies to be applied in the conservation of the nymphaeum.