The Grotta degli Animali, an artificial grotto located in the garden of Villa di Castello in Firenze, is a significant example of sixteenth-century Mannerist garden design. Commissioned by Cosimo I de’ Medici, the grotto was designed by Niccolò Pericoli (Il Tribolo) and later completed by Giorgio Vasari, with contributions from renowned artists such as Jean de Boulogne (Gianbologna) and Ammannati. Featuring marble fountains and animal sculptures symbolizing natural elements, the grotto’s hydraulic system once created the dramatic “Scherzo del Diluvio” water effect. Over the centuries, the grotto underwent multiple restorations, and recent work (completed in March 2024) utilized advanced digital documentation and 3D surveying techniques to reactivate the water features and improve its preservation. The project also integrated virtual reconstructions and addressed material degradation by creating a monitoring system for the grotto’s microclimate and structural health. Diagnostic surveys and advanced surveying methods, including laser scanning and photogrammetry, revealed key structural challenges and offered insights into the historical evolution of the water system. This work emphasizes the importance of monitoring semi-confined heritage environments like the Grotta degli Animali, where complex microclimatic conditions can lead to localized material deterioration. The CNR-ISPC, in collaboration with other institutions, has developed a methodological approach for diagnosing and monitoring such sites, focusing on assessing conservation states, identifying active decay processes, and predicting risks linked to environmental changes. Using non-destructive techniques like infrared thermography and moisture detection, along with the establishment of a digital twin of the grotto, the project aims to ensure long-term preservation. Continuous monitoring and analysis of microclimatic variations will inform conservation strategies, helping mitigate potential decay risks while supporting more sustainable preservation practices.