Summary 1. The relationship between hydrological connectivity, and the exchange processes of suspended sediments, organic matter and nutrients (NO3‐N) was investigated in a dynamically connected river–floodplain segment of the Danube over a 15‐month period in 1995 and 1996 in the Alluvial Zone National Park, Austria. 2. Based on water level dynamics and water retention times, three phases of river–floodplain connectivity were identified: disconnection (phase I), seepage inflow (phase II) and upstream surface connection (phase III). The frequency of occurrence of these phases was 67.5%, 29.3% and 3.2%, respectively, during the study period. 3. A conceptual model is presented linking hydrological connectivity with ecological processes. Generally, the floodplain shifts from a closed and mainly biologically controlled ecosystem during phase I to an increasingly open and more hydrologically controlled system during phases II and III. Phase I, with internal processes dominating, is designated the ‘biotic interaction phase’. 4. Phase II, with massive nutrient inputs to the floodplain yet relatively high residence times, and therefore, high algal biomass, is classified as the ‘primary production phase’. This demonstrates that water level fluctuations well below bankfull may considerably enhance floodplain productivity. 5. Finally, since transport of particulate matter is mainly restricted to short flood pulses above bankfull level, phase III has been defined as the ‘transport phase’. 6. The floodplain served as a major sink for suspended sediments (250 mt ha−−1 year−−1), FPOM (96 mt ha−−1 year−−1), particulate organic carbon (POC; 2.9 mt ha−−1 year−−1) and nitrate‐nitrogen (0.96 mt ha−−1 year−−1), but was a source for dissolved organic carbon (DOC; 240 kg ha−−1 year−−1), algal biomass (chlorophyll‐a; 0.5 kg ha−−1 year−−1) and CPOM (21 kg ha−−1 year−−1). Considerable quantities of DOC and algal biomass were exported to the river channel during phase II, whereas particulate matter transport was largely restricted to the short floods of phase III. 7. The Danube Restoration Project will create a more gradual change between the individual phases by increasing hydrological connectivity between the river channel and the floodplain, and is predicted to enhance productivity by maintaining a balance between retention and export of nutrients and organic matter.