A Dynamic Positioning system automatically maintains both the position and heading of a vessel by using its thrusters in the presence of external disturbances. This goal is ensured by a controller that compensates for the environmental disturbances and computes the proper set-points for each actuator. The core of such a system is composed of force and thrust allocation modules that tailor the required forces and moment over the available actuators. The propulsion systems used are often over-actuated and the thrust allocation algorithm implies an infinite number of solutions since it is impossible to solve analytically the problem. Over the years efforts from the research community dealt with the optimization in terms of accuracy, energy consumption, and maintenance with innovative allocation strategies were investigated. However, no publications or rules indicate the procedure for the evaluation of exhaust gas emission during dynamic positioning operations. For such a reason, the paper aims to develop an optimization procedure that includes an ad-hoc objective function with relative non-linear constraints for the thrust allocation logic that tends to minimize the actuators’ thrust. The procedure accounts for non-linear hydrodynamic effects on the thrust generation, including thruster-thruster and thruster-hull interactions, to obtain the most realistic results as possible. Moreover, following the IMO suggestions, the production of greenhouses gases emissions is evaluated in probabilistic terms. The proposed approach provides indicators in terms of yearly operability, fuel consumption, and environmental footprint during dynamic positioning operations that could be used for proper decisions in ship deployment.