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A large autonomous undersea vehicle (AUV), the Seahorse, has been designed, constructed, and tested by the Applied Research Laboratory at Pennsylvania State University (ARL/PSU, University Park, PA) for the U.S. Naval Oceanographic Office (NAVOCEANO, Stennis Space Center, MS). The vehicle is required to launch in shallow water (<10 m) and to hover without propulsion. Additionally, due to the very large size of the vehicle, low operating speeds and very long missions, small changes in vehicle trim resulting from battery replacement, sensor exchanges, and water temperature variations can result in significant drag-induced energy penalties over the duration of a mission. It is, therefore, important to continually maintain the AUV in fore-aft trim over the course of the mission. The vehicle is equipped with a two tank variable buoyancy system (VBS) to meet these requirements. The resulting control problem is one where the control variable, pump rate, is proportional to the third derivative of the sensed variable, depth; there are significant delays, and forces are nonlinear (including discontinuous) and highly uncertain. This paper describes the design of the VBS and the control software operating in two modes: depth control mode and trim control mode. In-water test data and simulation results are presented to illustrate the performance of the VBS controller. The benefits of the presented approach lie in the intuitiveness and simplicity of the design and the robustness as evidenced by the performance in both fresh and salt water. This paper provides practical insight into the operation of a VBS with an AUV and discusses actual operational experience. To our knowledge, no previous work considers the significance of an observed surface capture phenomenon to the design of a VBS control system, especially in very shallow water.