The colonization of periphytic algae in a temperate floodplain was studied in Lake Sakadaš, a part of a fluvial floodplain along the Danube River. An in situ investigation, using artificial substrata, was started after extremely high spring flooding and was carried out during long-lasting summer floods (July–August 2010). The physical and chemical environment was variable and large stands of metaphyton, submersed and floating macrophytes were spread along the lake. The periphyton development was initiated on the first day of exposition and algal abundance increased exponentially till day 27. Directional changes in the relative abundance of algal species, shown by the results of the non-metric multidimensional scaling, indicate a pattern of short-term sequences in algal colonization. The initial attachment of planktonic cyanobacteria and unicellular diatoms (initial phase, days 1–3) to the biofilm matrix was followed by the development of the filamentous chlorophytes, Cladophora glomerata and Oedogonium spp. (intermediate phase, days 6–15) and then by stalk-forming diatoms particularly Gomphonema spp. (late phase, days 18–33). According to the redundancy analyses, water temperature and oscillations of Danube water level that define the flooding pattern had the most significant influence on algal colonization. Flood-induced spreading of metaphyton firstly supported the rapid progress of algal colonization towards a climax community, while later, metaphyton together with macrophytes disrupted algal community by increasing the mechanical injuries, shading and grazing pressure. Consequently, algal abundance and community structure were returned to the intermediate phase of colonization.