Measurement, data transfer, modelling, controller systems are main subjects of interdisciplinary area during prototyping of marine automatic control systems. Experimental parameter identification under changing environmental conditions is an essential step for modelling and control system design are in question for various marine applications. The selection of variables to be measured, type of measurement sensors, type of control algorithms and controller systems, communication, signal conditioning are all important topics for parameter identification and real-time control applications in maritime engineering. The objective of this paper is to present brief review these important topics based on our case studies, such as ship roll motion reduction control, optimal trim control of a high speed craft, and dynamic position control of underwater vehicles. These projects involved extensive dynamic modelling, simulation, control algorithm design, real-time implementation and full-scale sea trials. In this paper, presented the methods, and the required characteristics of the marine control systems are proved with the results obtained by the simulation and test studies. Also, insight into the selection of hardware and software components for mechatronic applications in marine engineering is provided.