The study analyzes the succession process of the periphytic community in the bacterial, algal and protozoal fractions during the limnological periods of low water and high water in the lagoon system of Yahuarcaca, located in the floodplain of the Amazon River (Leticia, Colombia). Every 12 hours, for three days, three sheets of acetate per environment were collected (limnetic region and between macrophytes). The process of bacterial colonization for the low-water began at 12h with values ​​of 2.98E and ended with a decline of 2.57E + 06 - 1.32E + 06 cells / ml at 72h. For the period of high water there was an increase in the density. In the first stage of the algal colonization the two-dimensional genres predominated. In the second stage, Gomphonema affine, G. gracile, Melosira varians and Pinnularia sp.; and in the last phase, species such as Fragilaria aff. intermediate, F. aff. ulna, Aulacoseira varians, Oedogonium sp., Ulothix sp. and Nostoc sp. were found. Among the protozoa, the first settlers were flagellates, followed by free-living bacteriophage ciliates that gave way to fixed ciliates (vorticélidos type). Temperature and conductivity were the variables that had a closer relationship with the algal fraction, unlike the bacterial fraction, which dominated at the beginning of the process. For protozoa, the pH was the most influential factor in the presence and abundance during succession, presenting dominance toward the final hours during the two limnological periods. The decline and appearance of new species of algae at the final hours of the colonization process showed a change in the periphyton structure and a succession of the community in a span of 72 hours for this system in the Colombian Amazon. &nbsp