Underwater excavations require an immense amount of logistics and have inherent time limitations. Underwater challenges such as nitrogen toxicity, underwater color change, and dive time limits increase with working depths, affecting the interpretation of archaeological contexts. Thus, underwater excavations involve methods and approaches to extract the maximum information from small areas while providing a comprehensive understanding of the archaeological record. Here, we present the benefits of using an on-site laboratory comprising a microscope, binocular microscope, Fourier transform infrared spectrometer and blue light inspection device. Three case studies are presented, focusing on the identification of stratigraphic boundaries, as well as the preservation and identification of archaeological materials. The results show a complex stratigraphic sequence containing seven layers divided into four mineralogical units: (1) Calcite, (2) Calcite and aragonite, (3) Aragonite, and (4) Dolomite. Additionally, the use of an on-site laboratory is effective in preventing the misidentification of archaeological materials, which could affect the final interpretation of the archaeological site (e.g., glass, lead, bone), and enabling the identification of materials invisible to the naked eye, such as opaline phytoliths. In the case of the Antikythera shipwreck, the on-site laboratory facilitated the examination of stratigraphy and quality of the archaeological context while streamlining excavation practices and documentation. Furthermore, the on-site laboratory allowed for the assessment of material preservation and provide crucial insights to inform post-excavation treatments and analysis of artifacts.