Integrating geomatics remote sensing technologies, including 3D terrestrial laser scanning, unmanned aerial vehicles, and ground penetrating radar enables the generation of comprehensive 2D, 2.5D, and 3D documentation for caves and their surroundings. This study focuses on the Altamira Cave's karst system in Spain, resulting in a thorough 3D mapping encompassing both cave interior and exterior topography along with significant discontinuities and karst features in the vicinity. Crucially, GPR mapping confirms that primary vertical discontinuities extend from the near-surface (Upper Layer) to the base of the Polychrome layer housing prehistoric paintings. This discovery signifies direct interconnections helping with fluid exchange between the cave's interior and exterior, a groundbreaking revelation. Such fluid movement has profound implications for site conservation. The utilization of various GPR antennas corroborates the initial hypothesis regarding fluid exchanges and provides concrete proof of their occurrence. This study underscores the indispensability of integrated 3D mapping and GPR techniques for monitoring fluid dynamics within the cave. These tools are vital for safeguarding Altamira, a site of exceptional significance due to its invaluable prehistoric cave paintings.