Srebarna Lake, a UNESCO Biosphere Reserve and Danube floodplain wetland, is characterized by pronounced hydrological fluctuations related to variations in Danube River water levels. This study compared phytoplankton functional organization between selected historical and recent years using the Reynolds–Padisák functional group (FG) approach and considering variations in Danube water levels. The descriptive comparison included phytoplankton samples collected between May and September from the central lake area in three historical (2003, 2004, 2007) and four recent sampling years (2022–2025). Single-month observations from intervening years were also considered. Partial redundancy analysis (pRDA) was used to evaluate differences in FG composition between historical and recent periods in relation to measured environmental gradients, using a balanced subset of six years. The recent period was characterized by generally lower Danube water levels, suggesting reduced opportunities for hydrological connectivity with the Danube. Recurrent dominance of FG SN, represented by Raphidiopsis raciborskii, was observed in 2022–2024, contrasting with the prominence of S1 and contribution of FGs M and H1 in the historical observations. A strong reduction or disappearance of cyanobacterial FGs, accompanied by lower total phytoplankton biomass, occurred under contrasting hydrological extremes, with diatom FGs prominent in 2007 following flooding events and a predominance of FGs X1 and G in 2025 under severe low-water conditions. The overall pRDA model significantly explained variation in FG composition; however, the historical–recent contrast was not statistically significant when Period was tested separately at the whole-plot level, indicating that the observed temporal patterns should be interpreted in the context of interannual variation and the measured environmental gradients.

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