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There is ample evidence that tube‐dwelling invertebrates such as chironomids significantly alter multiple important ecosystem functions, particularly in shallow lakes. Chironomids pump large water volumes, and associated suspended and dissolved substances, through the sediment and thereby compete with pelagic filter feeders for particulate organic matter. This can exert a high grazing pressure on phytoplankton, microorganisms, and perhaps small zooplankton and thus strengthen benthic‐pelagic coupling. Furthermore, intermittent pumping by tube‐dwelling invertebrates oxygenates sediments and creates a dynamic, three‐dimensional mosaic of redox conditions. This shapes microbial community composition and spatial distribution, and alters microbe‐mediated biogeochemical functions, which often depend on redox potential. As a result, extended hotspots of element cycling occur at the oxic‐anoxic …