This paper describes methods for guidance, navigation and control of marine vessels to allow automatic maneuvering. The focus is on autonomous cooperation between vehicles in confined waters, like harbors or port entrances. Therefore, methods for centralized multi-vehicle trajectory generation are described considering static and dynamic obstacles. The optimized command values calculated by the trajectory generator are integrated within the vehicle dependent motion control system which has been designed as a two degrees of freedom structure. In that way, the feedforward control values can be applied efficiently with the manipulating signals created from robust local feedback controllers for velocity control and path following. The central guidance module is fed by synchronized navigation data while the controllers use data fused by a multi-sensor tightly coupled Kalman filter. The paper closes with experimental trials in the port of Rostock using two unmanned surface vehicles and an inflatable boat as interferer to validate the cooperation capabilities of the multivehicle system.