The submarine Marigondon Cave (MC) is not only one of the most spectacular diving caves but also an unstudied, submerged rock-shelter with potential for intact stratigraphy. The Marigondon Cave yielded two rock samples, one coral limestone fossil with a travertine mantle, and a sclerosponge specimen that provided evidence to understand the external and environmental conditions to which the cave might have been exposed. The study's aimed to determine the links between the cave's underwater conditions and the samples studied. Analytical methodologies such as IR spectroscopy, X-ray diffraction, Optical Microscopy, SEM/EDX and U-series isotope analyses were carried out to determine the chemical composition of two rock samples, and their crystal structures and formation ages. Results concluded that the two samples were composed mainly of the two calcium carbonate polymorphs calcite and aragonite; however, the sclerosponges contained a low percentage of Mg- calcite, illustrating a period of submergence. At other periods, Marigondon Cave would have been above water and favorable for Pleistocene fauna as well as possibly human settlement, as demonstrated by the travertine deposit on the coral limestone. This suggests that MC provides prospects for discovery of fossil assemblages that may be preserved in terrestrial deposits in the caves during periods of emergence. These periodic submersions conform to eustatic sea level changes during the past 130,000 years during the late Pleistocene and demonstrate that in that period a marine coral reef platform was the substrate within which the Marigondon Cave formed as a flank margin cave during nearly 80,000 years of emergence when sea level was lower than the present elevation of the cave.