Citation: Wagner, A., S. Volkmann, and P. M. A. Dettinger-Klemm. 2012. Benthic-pelagic coupling in lake ecosystems: the key role of chironomid pupae as prey of pelagic fish. Ecosphere 3(2):14. http://dx.doi.org/10.1890/ES11-00181.1Abstract. Studies of lake ecosystems have often treated benthic and pelagic habitats as discrete food chains with parallel, separated compartments. A limited number of studies on the importance of fish feeding for benthic-pelagic coupling have been conducted with a food-web perspective of lakes. We hypothesize that pelagic fish couple benthic and pelagic food webs by feeding on chironomid pupae ascending from the sediment to the surface. Over a two-year period, an analysis of the stomach contents of Eurasian perch (Perca fluviatilis L.) was combined with simultaneous catches of chironomids in near-bottom pupal traps and floating emergence traps exposed in the littoral and profundal region of a deep temperate reservoir. Chironomid larvae rarely served as prey for perch. While chironomid pupae from the littoral region were of minor importance as perch prey, we determined a substantial vertical trophic biomass transfer from the profundal to the pelagic food web for the pupation peak of profundal chironomids from May through June. During this period, chironomid pupae represented approximately 20-48% of the ingested biomass of all size classes of perch (70-340 mm). The pupae of only three large profundal species out of 84 chironomid taxa detected in the reservoir represented approximately 80% of the chironomids consumed by perch, indicating a key role for these taxa in benthic-pelagic coupling. The strong influences of species, habitat and size on the consumption of chironomid pupae by the pelagic perch provide the importance of detecting key benthic species that substantially contribute to the pelagic food web. The phenology of profundal species results in a seasonal shift in the feeding behavior of pelagic fish, which thereby influences the trophic dynamics of lake ecosystems. Therefore, we argue for a more integrated view of lake ecosystems that recognizes not only the littoral but also the complementarity of profundal and pelagic production pathways crucial for ecosystem functioning.