Rapidly varying fuel costs, environmental concerns and forthcoming emissions regulations impose a pressure on ships to operate in a more efficient, cost-effective and environmentally friendly way. The propulsion power and energy producing onboard installation- i.e. the marine energy system - is the main contributor to the overall cost-effectiveness, emissions footprint and efficiency of the vessel. To meet those stringent and often contradicting requirements, the sophistication and, hence, complexity of modern marine energy systems increases, while operating frequently at extreme conditions and close to the design limit. The challenge of making both existing and new marine energy systems more energy efficient and environmentally friendly imposes a need for new approaches for system configuration, design, operation and control that are able to consider the energy production and conversion onboard ships (fuel, mechanical, electrical, thermal) in an integrated manner. At the same time, simultaneous assessment of performance, safety, and reliability of marine systems, especially under real service conditions and transient operation modes are becoming increasingly important for both ship-owners and classification societies. To date, however, there is no formal methodological framework to cover the aforementioned needs in a holistic way. In this paper we present a novel approach for integrated dynamic process modelling and simulation of marine energy systems. Our methodology is based on the mathematical modelling of the dynamic thermofluid behaviour of components including energy conversion and rotating machinery such as heat exchangers, evaporators, compressors, turbochargers, pumps, valves, pipes, etc. The component process models are generic, reconfigurable, suitable for different types of studies and valid for a wide range of operating conditions. Then, following a hierarchical decomposition approach the lower-level component models are used to synthesise higher level subsystems and, in turn, complete energy systems. Experimental or service data are used for model verification and validation. The models are implemented in state of the art process modelling tools, where they are coupled with representations of operational scenarios/ profiles. In that manner we are able to perform a variety of model-based studies and applications like steady-state and dynamic simulation, design, optimisation and control of user-defined energy system configurations under realistic service conditions. The developed modelling framework aims at providing model-based decision support on: a) energy and emissions optimal design of onboard machinery, b) performance evaluation under real-service dynamic conditions for the whole mission envelope of the system, and c) assessment of the potential and operational capabilities of innovative designs. The main benefit from this holistic approach is that the steady-state design characteristics, off-design operational modes and dynamic/transient behaviour can be simultaneously assessed and/or optimised in a unified and consistent modelling framework. The presented approach can significantly aid the design process for new systems as well as the energy management, performance prognosis, and control optimisation and reconfiguration for existing vessels. The main characteristics and benefits of our methodology are illustrated via the dynamic modelling of a marine combined cycle system.