A novel underwater, open source, and configurable vehicle that mimics and leverages advances in quad-copter controls and dynamics, called the uDrone, was designed, built and tested. This vehicle was developed to aid coral reef researchers in collecting underwater spectroscopic data for the purpose of monitoring coral reef health. It is designed with an on-board integrated sensor system to support both automated navigation in close proximity to reefs and environmental observation. Additionally, the vehicle can serve as a testbed for future research in the realm of programming for autonomous underwater navigation and data collection, given the open-source simulation and software environment in which it was developed. This thesis presents the motivation for and design components of the new vehicle, a model governing vehicle dynamics, and the results of two proof-of-concept simulation for automated control.