In contrast to rivers, the effects of water level fluctuations on the biota are severely understudied in lakes. Lake Constance has a naturally pulsing hydrograph with average amplitudes of 1.4 m between winter drought and summer flood seasons (annual flood pulse (AFP)). Additionally, heavy rainstorms in summer have the potential to create short-term summer flood pulses (SFP). The flood pulse concept for lakes predicts that littoral organisms should be adapted to the regularly occurring AFP, ie taking advantage of benefits such as an influx of food sources and low predator pressure, though these organisms will not possess adaptations for the SFP. To test this hypothesis, we studied the aquatic invertebrate assemblages colonizing the gravel sediments of Lake Constance, the AFP in spring and a dramatic SFP event consisting of a one meter rise of water level in 24 h. Here, we introduce the term ‘hypolacustric interstitial’for lakes analog to the hyporheic zone of running water ecosystems. Our results confirm the hypothesis of contrasting effects of a regular AFP and a random SFP indicating that the AFP enhances the productivity and biodiversity of the littoral zone with benthic invertebrates displaying an array of adaptations enabling them to survive. The littoral zones of lakes deliver important ecosystem services by regulating flood effects, producing biomass and supporting biodiversity. To maintain and foster these services, the maintenance or reintroduction of natural water level fluctuations and the conservation of the habitat structures of the hypolacustric interstitial are urgently needed.