The flood pulse associated with local factors is the main drivers of the phytoplankton functional groups. The aim of this study was to evaluate the dynamics of the phytoplankton community and the Reynolds Functional Groups (RFG) and their relationships with the alternative states in a Pantanal floodplain lake. The Coqueiro Lake (municipality of Poconé, state of Mato Grosso, Brazil) was sampled monthly at three sites from April 2002 to May 2003. Three periods were identified: i) period I (first receding) with colonization of Egeria najas (Alismatales, Hydrocharitaceae), reduced depths and clear waters, characterized by the lowest species richness (mean = 23 taxa/sample) and reduced phytoplankton biomass (mean = 1.0 mg L-1); ii) periods II (low waters and rising) without Egeria najas, with lowest influence from the river, lowest depths, turbid waters, highest phytoplankton biomass (mean = 9.8 mg L-1) and species richness (mean = 29 taxa/sample); iii) periods III (high waters and beginning of the second receding) with Egeria najas and high influence from the river, greater depths, clear waters, with intermediate species richness (mean = 26 taxa/sample) and lowest phytoplankton biomass (mean = 0.7 mg L-1). Phytoplankton was composed mainly of nanoplanktonic algae with greatest contributions in the low waters without Egeria najas and was represented by 16 RFG, with reduced variability between the three periods and sites. The functional groups K, P, F, J, H1 and H2 were important in this shallow flood lake governed by natural mechanisms of alternation of clear water regime with reduced phytoplankton biomass to a new state of turbid water dominated by phytoplankton. The variations in the phytoplankton functional groups were related to the physical and chemical regime of the lake and the hydrodynamics of the flood system, which acts as a continuous renewal of the habitat conditions in the different alternative states the lake.