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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 500m and 1 km from the discharges. [ABSTRACT FROM AUTHOR]