In conventional electrically driven propulsion systems with fixed pitch propellers, thruster controllers are usually aimed at controlling propeller shaft speed only. Especially in unmanned marine vehicles which operate in dynamic flow conditions, these type thruster controllers provide unsatisfactory thrust responses. The reason for this is that the thrust force is simultaneously affected by dynamic effects like, variable ambient flow velocity and angle, thruster-thruster interaction and ventilation. It is aimed to achieve acceptable thrust tracking accuracy in all kind of dynamic flow conditions in this thesis work. A novel feed-back based thruster controller which includes the effect of incoming axial flow velocity, is designed for this purpose. In controller design, first, thruster propeller’s open water characteristics in four-quadrant flow states are measured. Data collected from open water tests are then non-dimensionalized and embedded in the controller’s thrust model code. Relation between ideal shaft speed and desired thrust is derived by using the four-quadrant propeller model. The proposed method is evaluated in the experimental test-setup designed for this study to simulate open water conditions. Results indicate that thrust tracking performance of novel controller is acceptable in all four-quadrant flow tests.