Nonlinear control of Autonomous Underwater Vehicles (AUVs) via the use of thrusters has been well established within the last 50 years. These AUVs can be used for various applications, including subsea inspection and maintenance, exploration, research, and observation. These thrusters are best suited for large thrust forces required by large movements, but are not optimal for fine control or in confined spaces. Research by our group into buoyancy control devices (BCDs) using reversible fuel cells (RFCs) has proven their viability and limitations. This thesis demonstrates nonlinear control of an AUV in the three dimensions directly controllable via BCDs while completing various mission profiles. An adaptive control law is derived that ensures stability throughout the completion of the desired mission. Simulation results demonstrate desired performance with low steady-state energy requirements.