The shipping industry is a major contributor to global greenhouse gas (GHG) emissions, which is why it is important to optimize every aspect of the efficiency of ocean-going vessels. This includes the antifouling paint that ensures hydrodynamic efficiency. Measuring the thickness of the antifouling on top of all other paint layers using THz cross-correlation spectroscopy (THz-CCS) underwater could enable vessel operators to monitor the state of the paint on ship hulls and plan any vessel’s sailing route and maintenance optimally. However, due to the high absorption of water in the THz domain, measuring through any significant amount of water is impossible, making a water removal method necessary. This study shows how a THz-CCS system can be packaged for underwater measurements using a molded silicone contact seal. In combination with a spectroscopic model for data treatment, the thickness of a single paint layer is retrieved underwater. This paves the way for a more advanced system capable of measuring multilayer maritime paint underwater, which will enable shipping companies to continuously monitor the paint layers’ thickness.