The term transitional waters encompasses a wide variety of ecosystems with highly variable environmental conditions and naturally impoverished biological communities. These characteristics have led to a considerable delay in the design and implementation of ecological assessment tools within the European Water Framework Directive. Chironomids are a very important faunal group of transitional waters in terms of relative abundance and species richness. In the present investigation a water quality index based on the chironomid pupal exuviae assemblages was developed. Thirty-seven sites were surveyed along the Catalonian coast (North-East Spain) for their Chironomid pupal exuviae. The index registered a significant response to the causes of eutrophication and its symptoms. Different taxonomic resolution levels were tested and a final tool is proposed based on a genus level identification of chironomid taxa and a classification system based on sensitive/tolerant taxa abundances. The tool has the advantage of being cost-effective (cheap, involving low time-consumption and easy to use) and of integrating all the habitats within the ecosystem.