AbstractThe dry phase of intermittent rivers promotes the accumulation of leaf litter on various terrestrial and aquatic habitats. This environmental heterogeneity causes a chemical diversification of leaf litter by a range of physical and biological degradation processes acting across the various habitats. After flow resumption, the chemically diversified leaves are mixed and subject to continued decomposition downstream. We hypothesized that the chemical diversification of leaf litter during the dry phase would affect leaf litter decomposition under re‐established lotic conditions. Our laboratory treatments mimicking dry‐phase habitats caused a strong chemical diversification of leaf litter, which—upon combination in mixed litter bags—accelerated its decomposition in a perennial river reach. We suggest that intermittent rivers may act as hotspots of organic matter diversification, with potential implications for organic matter processing at the river‐network scale.