Extensive fish production systems in continental areas are often created by damming headwater streams. However, these lentic systems favour autochthonous organic matter production. As headwater stream functioning is essentially based on allochthonous organic matter (OM) supply, the presence of barrage fishponds on headwater streams might change the main food source for benthic communities. The goal of this study was thus to identify the effects of barrage fishponds on the functioning of headwater streams. To this end, we compared leaf litter breakdown (a key ecosystem function in headwater streams), their associated invertebrate communities and fungal biomass at sites upstream and downstream of five barrage fishponds in two dominant land use systems (three in forested catchments and two in agricultural catchments). We observed significant structural and functional differences between headwater stream ecosystems in agricultural catchments and those in forested catchments. Leaf litter decay was more rapid in forest streams, with a moderate, but not significant, increase in breakdown rate downstream from the barrage fishponds. In agricultural catchments, the trend was opposite with a 2-fold lower leaf litter breakdown rate at downstream sites compared to upstream sites. Breakdown rates observed at all sites were closely correlated with fungal biomass and shredder biomass. No effect of barrage fishponds were observed in this study concerning invertebrate community structure or functional feeding groups especially in agricultural landscapes. In forest streams, we observed a decrease in organic pollution (OP)-intolerant taxa at downstream sites that was correlated with an increase in OP-tolerant taxa. These results highlighted that the influence of barrage fishponds on headwater stream functioning is complex and land use dependent. It is therefore necessary to clearly understand the various mechanisms (competition for food resources, complementarities between autochthonous and allochthonous OM) that control ecosystem functioning in different contexts in order to optimize barrage fishpond management.