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The summer phytoplankton community was studied across both vertical and temporal scales in relation to environmental factors in the shallow recreational Sava Lake. The sampling was conducted weekly at four depths from mid-July until mid-September 2014, in order to detect short-term changes within the assemblages. Besides physical and chemical parameters, meteorological data was also included in the investigation, as that year was characterized with extreme rainfall, which caused serious flooding in the region. The community succession was characterized by a reverse in the cyanobacteria (Codon M) and chlorococcal green algae (Coda F and J). Statistical analyses (RDA) indicated that changes in the community composition and successional pattern could have been due to the mixing regime variations in the reservoir, most likely induced by weather disturbances, especially high precipitation and wind events. These events did not permit massive cyanobacterial development, although they most likely caused resuspension of dissolved phosphorus from the sediment. When observing functional groups, three groups could be distinguished by their response to the above-mentioned parameters: the first prefers high temperature and insolation (Lm, Y, Lo, Xph, W2 and M), the second is correlated with precipitation and wind (Td, C, K, MP and X2), while the third group tolerates cloudiness (H1, F, N, X1, D, J and P).