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We investigated the effects of an experimental flood regime on periphyton and stream metabolism downstream of a large reservoir. Three floods took place in summer of 2000 and 2001 and two floods in summer of 2002. Residual flow in the River Spol was <2.5 m(3)s(-1). The experimental floods lasted 9 to 11 hours with peak flows ranging from 12 to 55 m(3)s(-1). Periphyton was collected in the River Spol (impact site) and in a reference stream in 1999 (pre-flood) and before and after each flood from 2000 to 2002. We measured ecosystem metabolism with the single station diel oxygen method a few days before and after floods in the River Spol. Floods temporarily reduced periphyton biomass, but the disturbance impact and recovery patterns were not uniform among floods, thus resulting in high inter-annual variation in seasonal biomass patterns. The average periphyton biomass in the River Spol even increased after a transient reduction in 2000. A principal component analysis indicated a persistent shift in the structure of the diatom community at the impact site. The floods reduced gross primary production and to minor extent ecosystem respiration, resulting in a transient decline in the P/R ratio. However, ecosystem metabolism recovered relatively fast. The new flow regime increased ecosystem dynamics, but it may take several years until the autotrophic energy base becomes adapted to the new and more dynamic flow regime.