In this thesis, we develop an approach to characterizing the uncertainty in energy use toward development of a real-time intelligent energy monitoring system for an autonomous under- water vehicle (AUV). The purpose of the intelligent energy monitoring system is to estimate current energy onboard the AUV, estimate energy needed to complete a desired mission, and to determine if and when the AUV should terminate the current mission and return to the recovery location due low energy reserves. In this work, we examine the relationship between water currents and energy used by the AUV, and we specifically address ways to characterize the relationship between uncertainty in water currents and uncertainty in energy use. We also examine the development of a battery model for the AUV, and test this model under simulated and real world conditions. We also develop a model for predicting future energy states, and evaluate this model using real world trials.