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1. The efficacy of leaf-litter decomposition, sediment respiration, biofilm biomass, growth, chlorophyll a concentration and the autotrophic index (biofilm ash-free dry mass/chlorophyll a) and fungal biomass for detecting human-induced change was evaluated using 24 references and 15 disturbed stream sites located in central Portugal.

2. Decomposition rates of alder (Alnus glutinosa) and oak (Quercus robur) leaves and sediment respiration rates were effective in discriminating impairment. Decomposition was negatively correlated with abiotic factors, such as ammonium and nitrite concentrations, connectivity and alterations in the hydrological regime, and positively correlated with nitrate concentration and oxygen concentration. Sediment respiration rates were correlated with organic contamination, land use and morphological changes.

3. Growth rates of biofilm, concentration of chlorophyll a and the autotrophic index, although 41-73% higher at disturbed compared to reference sites, were not significantly different. These three variables were significantly correlated with total organic carbon, oxygen concentration, pH, nitrite and the presence of dams. Fungal biomass on leaves and biofilm biomass on natural substrata did not differ between reference and disturbed sites.

4. Our findings lend support to the use of functional variables like decomposition and sediment respiration in monitoring and when used together with structural variables should give a more holistic measure of stream health.