A set of guidelines are presented for the definition of monitoring plans in coastal and transitional (estuarine and lagoonal) systems subject to the European Union Water Framework Directive - WFD (2000/60/EC). General principles of best practice in monitoring are outlined, including (a) the definition of three types of broad management objectives: water quality, conservation, and human use, to which the general public may easily relate. These will define the core and research indicators (WFD quality elements) to be used for monitoring; (b) priorities and optimisation in a (financially and logistically) resource-constrained environment; (c) quality assurance; and (d) assessment of monitoring success: this should focus on the outputs, i.e. the internal audit of the monitoring activity, and on the outcomes. The latter component assesses programme effectiveness, i.e. environmental success based on a set of clearly-defined targets, and informs management action. The second part of this work discusses the approach and actions to be carried out for implementing WFD surveillance, operational and investigative monitoring. Appropriate spatial and temporal scales for surveillance monitoring of different indicators are suggested, and operational monitoring is classified into either screening or verification procedures, with an emphasis on the relationship between drivers, pressure, state and response. WFD investigative monitoring is interpreted as applied research, and thus guidelines cannot be prescriptive, except insofar as to provide examples of currently acceptable approaches. Specific case studies are presented for both operational (coastal eutrophication control) and investigative monitoring (harmful algal blooms), in order to illustrate the practical application of these monitoring guidelines. Further information is available at http://www.monae.org/ .