Large dams regulate river hydrology and influence water chemistry, sediment dynamics, channel form and biotic communities. These effects may translate into important changes in river ecosystem processes, especially in rivers naturally subject to strong seasonality, such as those under Mediterranean climate. The effects of flow regulation on ecosystem metabolism [i.e. gross primary production (GPP) and ecosystem respiration (ER)] were analysed by means of open-stream measurements. Organic matter accrual and metabolism were measured in reaches upstream and downstream from large reservoirs in three tributaries of the Ebro River (NE Iberian Peninsula) during three sampling campaigns. Dams reduced downstream hydrological variability, dampened floods and increased the duration of interflood periods. Benthic organic matter increased twofold and chlorophyll-a eightfold. GPP increased by 59% on average, whereas ER increased by 75%. In general, flow regulation intensified the capacity of downstream river reaches to store and process materials and energy, therefore increasing the amount of organic carbon processed and altering the whole flux of materials and energy along the river continuum ; This research was supported by the Spanish Ministry of Economy and Competitiveness through the project SCARCE Consolider-Ingenio CSD2009-00065. The compilation of environmental data was possible thanks to the Water Agencies of Ebro and the Water Agency of Catalonia. Laurie Boithias, Anna Giorgi, Lorea Flores and Lampros Nakis provided support in the field or in the laboratory. We also want to acknowledge financial support in terms of pre-doctoral grants from the University of the Basque Country (I. Aristi), the Basque Government (M. Arroita), as well as a postdoctoral grant ‘Juan de la Cierva’ (jci-2009-05604 and jci-2010-06397) (D von Schiller) and a Marie Curie European Reintegration Grant (PERG07-GA-2010-259219) (V Acu~na). This work was partly supported by the Generalitat de Catalunya (Consolidated Research Group 2009 SGR-00759) and the Basque Government (Consolidated Research Group: Stream Ecology 7-CA-18/10)