During the past decade, basic hydrological conditions of a floodplain lake in the middle Danube section have been altered with long-lasting extremely high flooding. The objective of the paper is to show the effectiveness of the functional approach to explain phytoplankton changes associated with hydrological events. Intensity and duration of flooding were qualified as the primary cause for the changes of functional groups. Flooding phase was characterised by diatoms (B, C, D, P, T B ) tolerant to water column mixing. Due to the dilution and washout effect their biomass was low during the long-lasting flooding despite their input from the river. Co-occurrence of coccoid green algae (X1, J, F) was associated with turbid and mixed waters. High-nutrient concentrations and water column stability during the long-term dry conditions led to the dominance and high biomass of cyanobacteria. Low-nitrogen H1 group was particularly sensitive to stress caused by flooding, while filamentous N2-fixing (S N ) and non N2-fixing species (S1) showed tolerance to short-term flooding. The development of euglenoids and dinoflagellates (W1, W2, L O ) was also associated with dry conditions and seasonal changes in autumn. The functional classification allows representing of the hydrological phases which characterise the phytoplankton succession in highly disturbed river-floodplain systems.