Exploring and surveilling the marine environment away from shore is critical for scientific, economic, and military purposes as we progress through the 21st century. Until recently, these missions far from shore were only possible using manned surface vehicles. Over the past decade, advances in energy density, actuators, electronics, and controls have enabled great improvements in vehicle endurance, yet, no solution is capable of supporting persistent operation especially when considering power hungry scientific surveys. This dissertation summarizes contributions related to the development of an adaptable underwater docking station and associated navigation solutions to allow applications in the wide range of maritime missions. The adaptable docking system is a novel approach to the standard funnel shaped docking station design that enables the dock to be collapsible, portable, and support a wide range of vehicles. It has been optimized and tested extensively in simulation. Field experiments in both pool and open water validate the simulation results. The associated control strategies for approach and terminal homing are also introduced and studied in simulation and field trials. These strategies are computationally efficient and enable operation in a variety of scenarios and conditions. Combined, the adaptable docking system and associated navigation strategies can form a baseline for future extended endurance missions away from manned support.