Ancient ceramics recovered after a long burial period have probably undergone several alterations and contaminations, introducing a chemical variability, affecting the ceramic’s natural variability. That is, the chemical and the mineralogical compositions of the ceramic pastes after their deposition will not be the same as they originally were. Therefore, it is known that the alteration and contamination processes, and the discrimination of some elements, should be considered when studying the ceramics to avoid incorrect interpretations about their provenance, technology and the use of the artefact, as well as its proper preservation. In the present work, the authors performed an experimental approach in order to study the alterations and contaminations that occurred in 60 ceramic cylinders buried in two different underwater environments. Once the pieces were taken out from the water environments, they were characterized by a multi-analytical approach. For this purpose, inductively coupled plasma mass spectrometry (ICP-MS), X-ray diffraction (XRD), scanning electron microscopy–energy dispersive spectrometry (SEM–EDS) and Raman spectroscopy were used. Newly formed minerals of different forms have been identified, with different crystallization grades. Some examples are the needles, flakes, sponges and long and short prisms composed of several elements such as Ca, F, S and O.