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Ecosystem functioning and community structure are recognized as key components of ecosystem integrity, but comprehensive, standardized studies of the responses of both structural and functional indicators to different types of anthropogenic pressures remain rare. Consequently, we lack an empirical basis for (i) identifying when monitoring ecosystem structure alone misses important changes in ecosystem functioning, (ii) recommending sets of structural and functional metrics best suited for detecting ecological change driven by different anthropogenic pressures, and (iii) understanding the cumulative effects of multiple, co-occurring stressors on structure and function. We investigated variation in community structure and ecosystem functioning of stream ecosystems along three gradients (10–16 independent stream sites each) of increasing impact arising from agriculture, forestry and river regulation for hydropower, respectively. For each stream, we quantified variation in (i) the abiotic environment, (ii) community composition of four organism groups and (iii) three basal ecosystem processes underpinning carbon and nutrient cycling in streams. We assessed the responsiveness of multiple biodiversity, community structure and ecosystem functioning indicators based on variance explained and effect size metrics. Along a gradient of increasing agricultural impact, diatoms and fish were the most responsive groups overall, but significant variation was detected in at least one aspect of community composition, abundance and/ or biodiversity of every organism group . In contrast, most of our functional metrics did not vary significantly along the agricultural gradient, possibly due to contrasting, antagonistic effects of increasing nutrient concentrations and turbidity on ecosystem process rates. The exception was detritivore-mediated litter decomposition which increased up to moderate levels of nutrient. Impacts of river regulation were most marked for diatoms, which were responsive to both increasingly frequent hydropeaking and to increasing seasonal river regulation. Among functional indicators, both litter decomposition and algal biomass accrual declined significantly with increasing hydropeaking. Few structural or functional metrics varied with forest management, with macroinvertebrate diversity increasing along the forestry gradient, as did algal and fungal biomass accrual. Together, these findings highlight the challenges of making inferences about the impacts of anthropogenic disturbances at the ecosystem level based on community data alone, and pinpoint the need to identify optimal sets of functional and structural indicators best suited for detecting ecological changes associated with different human activities.