Rivers receive substantial amounts of terrestrial organic carbon and a large fraction is released as CO2 or CH4 to the atmosphere. Global estimates of CO2 or CH4 emissions from inland waters are based on perennial rivers, although more than half of the global river length is prone to flow intermittence (lacking flowing water part of the year). The contraction of the flowing phase, with final fragmentation of river networks by drying of non-perennial reaches, can reduce or promote emissions at the local-(river reach) or regional-(river network) scale. We quantified CO2 and CH4 emissions from flowing water and dry riverbeds across six European drying river networks (DRNs, 120 reaches) and three seasons providing a unique dataset with 443 measurements. We identified drivers of emissions among local and regional variables and metrics describing local drying patterns and network-scale fragmentation. We also upscaled net CO2 emissions to the 6 DRNs and annual timescale. CO2 and CH4 emissions from flowing water in non-perennial reaches were affected by drying severity indicating a legacy effect, even after flow resumption. At the network scale, dry riverbeds contributed to annual emissions up to 77%, indicating an urgent need to include non-perennial rivers when assessing global greenhouse gas emissions.

Disturbance and connectivity control biodiversity, ecosystem functioning and their interactions across connected aquatic and terrestrial ecosystems, that form a meta-ecosystem. In rivers, detrital organic matter (OM) is transported across terrestrial-aquatic boundaries and along the river network and decomposed on the way by diverse communities of organisms, including microorganisms and invertebrates. Drying naturally fragments most river networks and thereby modify organism dispersal and OM transfers across ecosystems. This may prevent organisms from reaching and consuming OM, generating mismatches between community composition and decomposition. However, little evidence of the effects of drying on river network-scale OM cycling exists. Here, we aim to examine the effects of fragmentation by drying on the structure of consumer communities and ecosystem functioning within interacting aquatic-terrestrial river ecosystems. We monitored leaf resource stocks, invertebrate communities and decomposition rates in the instream and riparian habitats of 20 sites in a river network naturally fragmented by drying. Although instream resource quantity and quality increased with drying severity, decomposition decreased due to changes in invertebrate communities and particularly leaf-decomposer abundance. Invertebrate-driven decomposition peaked at intermediate levels of upstream connectivity, suggesting that intermediate levels of fragmentation can promote the functioning of downstream ecosystems. We found that the variability in community composition was unrelated to variability in decomposition at sites with low connectivity and high drying severity, suggesting that such conditions can promote mismatches between community composition and decomposition. Decomposition instream was correlated to decomposition in the riparian area, revealing one of the first network-scale evidence of the links between ecosystem functions across terrestrial-aquatic boundaries. Our river network-scale study thus demonstrates the paramount effect of drying on the dynamics of resources, communities and ecosystem functioning in river networks, with crucial implications for the adaptive management of river networks and preservation of their functional integrity.