Organisms often respond in similar ways to environmental or spatial gradients, particularly at large spatial scales, but patterns at finer scales and across ecotones are less certain. It is important to understand these relationships at multiple spatial scales, as managers often need suitable surrogate taxa for conservation and monitoring purposes. We explored whether community concordance at the river-riparian interface was decoupled by increasing anthropogenic stress (a gradient of local land-use intensity) at 15 sites over three years within the LTER site, Rhine-Main Observatory, a low mountain river system in central Germany. We assessed concordance between four organism groups: riparian spiders and carabid beetles, benthic macroinvertebrates, and combined aquatic macrophytes and riparian plants. This represented three different linkages: (1) predator-prey, (2) direct competition, and (3) habitat associations. While there were no correlations in richness patterns, multivariate community structure was highly concordant between all groups. Anthropogenic stress strongly reduced links between riparian spiders and carabid beetles, likely resulting from their shared resource requirements. However, increasing concordance occurred between plants and other groups. We posit that patterns may be resulting from two processes: (1) linkages between directly competing species decouple with increasing anthropogenic stress, and (2) stronger coupling may occur between habitat providers and dependent species when overall habitat complexity is reduced. These results highlight the complex manner in which anthropogenic stress can influence ecosystems and the importance of considering community structure when exploring biodiversity patterns in basic and applied ecological research, particularly at small scales and for surrogate taxa development.