Rivers form meta-ecosystems, in which disturbance and connectivity control biodiversity, ecosystem functioning, and their interactions – across the river network, but also across connected instream and riparian ecosystems. This aquatic-terrestrial linkage is modified by drying; a disturbance that also naturally fragments river networks and thereby modifies organism dispersal and organic matter (OM) transfers across the river network. However, little evidence of the effects of drying on river network-scale OM cycling exists. Here, we assessed the effects of fragmentation by drying at the river meta-ecosystem scale by monitoring, leaf resource stocks, invertebrate communities, and decomposition rates across three seasons and 20 sites, in the instream and riparian habitats of a river network naturally fragmented by drying. Although instream leaf resource quantity and quality increased, leaf-shredder invertebrate richness and abundance decreased with flow intermittence. Decomposition was however mainly driven by network-scale fragmentation and connectivity. Shredder richness and invertebrate-driven decomposition both peaked at sites with an intermediate amount of intermittent reaches upstream, suggesting that upstream drying can promote the biodiversity and functioning of downstream ecosystems. Shredder richness had however a negative effect on decomposition in perennial sites, likely due to interspecific competition. Leaf quantity, invertebrate communities, and invertebrate-driven decomposition became more similar between instream and riparian habitats as drying frequency increased, likely due to homogenization of environmental conditions between both habitats as the river dries. Our study demonstrates the paramount effects of drying on the dynamics of resources, communities, and ecosystem functioning in rivers and represents one of the first network-scale evidence of the co-drivers of ecosystem functions across terrestrial-aquatic boundaries.