Abstract Long‐term dynamics of phytoplankton have been addressed in marine and lake systems, but rarely in rivers. Large rivers, however, are highly human‐impacted, whereas global warming may further affect the functioning of phytoplankton at long‐term scale. In the middle section of the large European Danube River, long‐term decrease in phytoplankton biomass (Chl‐a) and increase in species diversity have formerly been revealed. The functional community composition that relates to ecosystem functioning directly has not been addressed previously. We analyse a 34‐year‐long phytoplankton data set from the middle river section at Göd (N‐Budapest), Hungary. We focus on gradual changes in the functional composition and functional diversity components based on the functional trait and functional group approaches. We hypothesised that long‐term gradual changes in major environmental constraints should be followed by gradual shifts in dominance relationships among functional traits and functional groups of phytoplankton. We further hypothesised that functional shifts were highlighted by gradual changes in functional diversity components: evenness, divergence and dispersion. Water discharge of the middle Danube shifted towards the more frequent occurrence of lower values. On the other hand, high floods (>3,000 m3/s) increased significantly with shortening tendency in duration and altered seasonality. The concentration of N and P forms, as well as total suspended solids decreased significantly. Water temperature increased significantly, especially in summer. In the phytoplankton, single‐celled eutrophic centric diatoms decreased in relative abundance, but flagellated, elongated and filamentous forms increased. A clear functional shift was the dominance decrease in planktonic taxa and the relative abundance increase in benthic diatoms. All functional diversity components increased significantly in the entire data set, except functional evenness (FEVE) based on the functional group approach. At seasonal scale, all significant trends showed increases, except the FEVE components of the functional group approach, which decreased in winter and spring significantly. Long‐term increase in functional diversity components alone could indicate enhanced ecosystem functioning of phytoplankton in the middle section of the Danube. However, we argue that the observed increase in functional diversity may be related to a gradual shift from high‐biomass communities with the dominance of eutrophic centric diatoms towards the relative increase in several, but low‐biomass elements. These include a few planktonic algae well adapted to the altered conditions, diatoms with benthic origin and dispersed limnophilic taxa. Our results provide the first evidence for a long‐term phytoplankton functional regime shift in a European large river. Global warming, human impacts and oligotrophication might potentially increase the functional diversity of large river phytoplankton, but the origin and functional role of taxa should carefully be considered. The observed functional shift in phytoplankton might also be indicative for alterations in the food‐web structure of the middle section of the Danube River at long‐term scale.
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