Abstract Chemical pollution is one of the greatest threats to freshwater ecosystems, especially in Mediterranean watersheds, characterized by periodical low flows that may exacerbate chemical exposure. Different groups of emerging pollutants have been detected in these basins during the last decade. This study aims to identify the relationships between the presence and levels of prioritary and emerging pollutants (pesticides, pharmaceutical active compounds—PhACs, Endocrine Disrupting Compounds EDCs and Perfluorinated Compounds—PFCs) and the invertebrate community in four Mediterranean basins: the Ebro, the Llobregat, the Júcar and the Guadalquivir. Structural (species composition and density) and functional (catalase activity of the tricopteran Hydropsyche exocellata and the feeding activity of the cladoceran Daphnia magna) variables were analyzed to determine which of the pollutants would greatly influence invertebrate responses. EDCs and conductivity, followed by PhACs, were the most important variables explaining the invertebrate density changes in the studied basins, showing a gradient of urban and industrial pollutions. Despite this general pattern observed in the four studied basins – impoverishment of species diversity and abundance change with pollution – some basins maintained certain differences. In the case of the Llobregat River, analgesics and anti-inflammatories were the significant pollutants explaining the invertebrate community distribution. In the Júcar River, fungicides were the main group of pollutants that were determining the structure of the invertebrate community. Functional biomarkers tended to decrease downstream in the four basins. Two groups of pollutants appeared to be significant predictors of the catalase activity in the model: EDCs and PhACs. This study provides evidence that the information given by functional biomarkers may complement the results found for the structural community descriptors, and allowed us to detect two emerging contaminant groups that are mainly affecting the invertebrate community in these basins.