This investigation analyzed the variation of the phytoplanktonic assemblage in the main water body of the swamp system of Ayapel (Cordoba), Colombia in different periods from the hydrological pulse. The results in six field periods between September 2004 and June 2005 and in five sampling stations showed that the structure and dynamics of the assemblage and physical and chemical variables vary in relation to the hydrological pulse. In general terms 37 taxa were registered, being Cylindrospermopsis raciborskii and Lyngbya cf. limnetica the most important taxa. The variations in the structure of the assemblage, presented greater in the dry periods and in the transition to rain period.