Most methods for assessing the ecological status of streams focus on structural characteristics (water quality, community composition, riparian vegetation) but neglect functional properties of the ecosystem because routine methods to assess stream function are scarce. Metabolism, one of the most integrative ecosystem functions, can be a good indicator of stream function because it is relevant across all sizes and types of streams, is sensitive to stressors, such as eutrophication or changes in riparian cover, and can be measured continuously. Environmental controls on whole-ecosystem metabolism were measured at 19 contrasting stream reaches in the Basque Country (northern Spain). Discharge, temperature, and O₂ were monitored continuously for 15 mo, reaeration rate was calculated with the nighttime regression method, and whole-stream metabolism was calculated by the single-station open-channel method. The effect of discharge on reaeration coefficients was highly site-specific. Average gross primary production (GPP) ranged from 2.7 to 11.0 g O₂ m⁻² d⁻¹, was highest at eutrophic sites, and showed no relationship with periphyton biomass. Ecosystem respiration (ER) ranged from 6.3 to 42.6 g O₂ m⁻² d⁻¹ and was highest at polluted sites. Differences among sites increased in summer. All sites were heterotrophic on an annual basis, but 3 were autotrophic during summer. Turbidity was the main controller of primary production during summer and explained 20% and 39% of the spatial variation in GPP and net ecosystem production, respectively. Biological O₂ demand of water explained 40% of ER variance. Catchment activities also controlled GPP, which decreased as population density increased. To our knowledge, our study is the first report of continuous monitoring of whole-stream metabolism at many reaches simultaneously, and it shows the potential of this technique for routine monitoring of stream function.