Floods are necessary for the functioning of floodplain ecosystems. Ultimately, flood effects on biota are spatially complex and unfold at various time scales. Yet, biodiversity conservation in regulated floodplains requires a sound quantification of the main pathways how floods affect riverine ecosystems. Here, we investigated the relative effects of flood frequency, magnitude, and time elapsed since the last flood on macroinvertebrate communities of 24 parafluvial habitats in the Maggia river floodplain, Switzerland. Parafluvial habitats were sampled seasonally over 1 year, and a combination of 2D hydrodynamic modelling and piecewise structural equation modelling was used to quantify the direct and indirect effects of local hydrological metrics on macroinvertebrate communities. We found that high flood frequency favoured rheophilic species (EPT taxa) over other groups (Coleoptera, Diptera) and prevented strong competitive interactions and competitive exclusion by maintaining low food resource levels. Importantly, we found that parafluvial habitats exhibited more lentic-like characteristics as time passed after a flood, which caused EPT taxa to be relatively more abundant and taxa richness higher immediately after flood disturbance. Lastly, overall taxa richness increased over time after a flood and even more so after larger floods. Our results suggest that variation in flood magnitude, frequency, and return period maximizes beta diversity within floodplain riverscapes due to the independent and spatially interactive responses of parafluvial habitats.