The role of hydromorphological degradation and temporal variation for food webs in human-modified rivers is still not fully evaluated. We tested the hypothesis that man-made engineering structures alter macroinvertebrate resource use in the Elbe River (Germany) in relation to seasonal variation. Stable isotopes (δ¹³C, δ¹⁵N) and mixing models revealed that dietary contributions of benthic organic matter (BOM) and phytoplankton were driven by engineering structure. Contributions of biofilm were driven by season, while contributions of terrestrial particulate organic matter (t-POM) were driven by both engineering structure and season. Contributions of t-POM were larger than those of phytoplankton in spring and summer, but not in autumn, which adds to the debate about the sources of organic matter fuelling riverine benthic food webs. Resource availability was not systematically related to resource use, indicating that factors other than resource limitation were responsible for the observed results. By demonstrating that human alterations determine consumer resource use independently from resource availability, our study links hydromorphological modifications to fluxes of matter in riverine food webs. Future studies should quantify organic matter fluxes from various autochthonous and allochthonous pathways in human-modified and natural rivers to allow for a robust synthesis of how hydromorphological modifications alter benthic food webs.