Integrated monitoring of South Portugal water bodies: a methodology towards WFD F. A. Martins, J. Janeiro, S. Gabriel, A. Vena ˆ ncio and R. Neves ABSTRACT F. A. Martins J. Janeiro S. Gabriel A. Vena ˆ ncio CIMA, EST-Universidade do Algarve, Campus da Penha, Faro, Portugal E-mail: fmartins@ualg.pt; janeiro.jm@gmail.com; smgabriel@ualg.pt; avenancio@ualg.pt R. Neves MARETEC, IST-Universidade Te ´ cnica de Lisboa, Av. Rovisco Pais, Lisboa, Portugal E-mail: ramiro.neves@ist.utl.pt The challenge on implementation of the EU Water Framework Directive (WFD) (2000/60/EC) fosters the development of new monitoring approaches. The directive promotes the use of modelling techniques to assist all phases of the process, from characterization and establishment of reference conditions to identification of pressures and assessment of impact. This work is based on the above principles. A classical monitoring of the water status of the main transitional water bodies of Algarve (South of Portugal) is combined with advanced in situ water profiling and hydrodynamic, water quality and ecological modelling to build a complete description of the system. The aim is to demonstrate a methodology where traditional monitoring and modelling tools can be joined together to draw a holistic picture. The results show that globally the water bodies present a good trophic status. Eutrophication symptoms are not generalized. Due to physical transport and dispersion, nutrient enrichment is not the only factor limiting growth; residence time is also an important factor. Some confined regions with high residence times are at present endangered by point and diffuse sources of pollution. The microbiologic impact of waste water treatment plants (WWTP) is confined to regions between 500 m and 1 km from the discharges. Key words | Arade Estuary, Guadiana Estuary, integrated monitoring, numerical model, Ria Formosa, water framework directive INTRODUCTION The main goal of the WFD is to achieve good ecological status across European surface waters by 2015. Monitoring is a key tool to this objective. It is required to cover a number of ‘water quality elements’ including, physico-chemical, hydro-morphological, biological and chemical parameters. Three monitoring modes are specified: “surveillance” to assess long-term changes and provide baseline data, “oper- ational” to provide additional data on water bodies at risk or failing good ecological status and “investigative” to assess the causes of such failure. To succeed in this intent it is necessary to adopt a holistic ecosystem based approach. It is necessary to change the present monitoring practices and move from ‘station-oriented monitoring’ to ‘basin or system- oriented monitoring’ (de Jonge et al. 2006). Progress will be made if the collected information is integrated and aggre- gated in valuable tools such as structure- and functioning- oriented computer simulation models and Decision Support Systems. The price of the monitoring effort will ultimately be the factor controlling the degree of detail obtained. It is thus important to use newer and more economic techniques (Allan et al. 2006). The use of portable underway water quality monitoring systems is one possibility and is now starting to be used (Hodge et al. 2005). Numerical models can be used to further extend the measurement campaigns in space and time (Gohin et al. 2005). Moreover, numerical models help to understand the processes controlling the system and the impact of management actions (Martins et al. 2003). WFD has caused an important impulse in both doi: 10.2166/wst.2009.509 1979 Q IWA Publishing 2009 Water Science & Technology—WST | 60.8 | 2009