On the surface of the Cave of Altamira’s prehistoric paintings, a series of active deterioration processes are evident, leading to significant alterations of this invaluable heritage. This study proposes a comprehensive methodology for the systematic recording and management of these alterations. To achieve this, advanced microphotogrammetric monitoring techniques are employed, allowing for the acquisition of very high-resolution images that provide objective and quantifiable data that let us determine the evolution of the alterations. By comparing these images with those from earlier campaigns, the study tracks changes. The data collected through this protocol has helped with the development of new research avenues to understand, among the many alteration processes that impact paintings, the dynamics of water and fluid mechanics affecting the conservation of Cave of Altamira. These investigations help clarify how, why, and at what rate degradation processes such as pigment migration, washing, and bacterial colonization occur. The insights gained from these techniques inform indirect conservation measures aimed at reducing the deterioration of the cave art, located both on the Polychrome ceiling and throughout the rest of the Cave of Altamira. The results underline the importance of regular monitoring and the application of precise, non-invasive techniques to protect rock art from continued degradation. This research provides a model for similar conservation initiatives at other vulnerable heritage sites.