Stream and riparian habitats are meta-ecosystems that can be strongly connected via the emergence of aquatic insects, which form an important prey subsidy for terrestrial consumers. However, human perturbations that impact these habitats may propagate across traditional ecosystem boundaries, thus disrupting aquatic-terrestrial food web linkages. We investigated how algal production, aquatic invertebrates, and terrestrial spiders influence cross-ecosystem connectivity in temperate streams across four European case-study basins with varying levels of human disturbance. We used fatty acid biomarkers to measure putative aquatic linkages to riparian spiders. Variation partitioning analysis indicated that aquatic insect dispersal traits explained a relatively large proportion of variability in the fatty acid profile of riparian arachnids. Trophic connectivity, as measured by the proportion of the polyunsaturated fatty acid eicosapentaenoic acid (EPA), was positively associated with abundances of ‘aerial active’ dispersing aquatic insects, although this influence was shared with changes in environmental context and arachnid beta diversity. Structural equation modelling helped further demonstrate how aquatic insect communities influence trophic connectivity with riparian predators after accounting for biological and environmental contingencies. Our results further suggest that inputs of stream insects are a source of essential fatty acids for adjacent terrestrial food webs. Gradients in riparian vegetation structure alter aquatic-terrestrial food-web linkages by increasing subsidy quality despite reducing primary production. Consequently, ecosystem properties such as woody riparian buffers that enhance aquatic-terrestrial connectivity have the potential to affect a wide range of consumers in modified landscapes.