Ambitious goals set for all EU states in the water framework directive call for the development of appropriate tools that support the implementation of the directive. Mathematical modelling can be utilised for devising the methodologies that address its many aspects, from evaluation of management alternatives to design of operational monitoring programmes. A major difficulty is the lack of detail in the directive regarding the implementation of monitoring programmes. This paper reviews and discusses the role of modelling in the implementation of the directive, with particular emphasis on integration of modelling into directive monitoring systems. New approaches, such as the Bayesian maximum entropy method, are discussed. The method utilises models in the processes of waterbody mapping and assessment and optimisation of water quality monitoring programmes; the authors are currently implementing the method to Irish coastal waterbodies. It is concluded that one of the main difficulties in implementing the directive is the lack of a structured approach in the development and management of monitoring programmes; mathematical models are recommended tools to help overcome these difficulties.