Modeling and control of remotely operated underwater vehicles is a challenging problem that depends greatly on how the dynamics of their thrusters are compensated. In this thesis a novel method for characterizing thruster dynamics using a six-axis load cell is presented. Multiple dynamic models are characterized with this test setup. Model-based control design strategies are used to compensate for nonlinearities in the dynamics, which include input dead zones and coupling with fluid dynamics. Multiple estimation methods are presented to construct an estimate of fluid velocity which is handled as an unmeasured state. The different models, controllers, and estimators are comparatively evaluated in closed-loop experiments using the six-axis load cell to measure thrust tracking performance. Full vehicle simulations using the experimentally characterized models provide additional opportunities for comparison of control and estimation strategies. The potential tracking control benefits from the variety of presented thruster dynamics compensation strategies are evaluated for a remotely operated underwater vehicle with multiple thrusters.