The flood pulse of black water rivers in the Amazon basin determines the composition of species along the flood gradient in igapó forests. The Balbina dam, built on the Uatumã River, has altered the flood pulse and caused changes in the floristic composition of adult trees throughout the downstream area. There is a lack of studies on how communities of seedlings in igapó forests respond to changes in the flood pulse. This study investigates the response of seedling communities in the igapó forest downstream the Balbina dam and compares it with two pristine areas. The areas were sampled with transects of 1x25 m within 36 plots (25x25 m) along the flood gradient. Richness and dominance were calculated by simple regression and ordination analyses. The pristine areas had the same pattern of richness, dominance and genera distribution along the flood gradient. However, the affected Uatumã area formed different groups of genera by NMDS analysis, which divided them along the flood gradient with significantly increased dominance of three genera. The insertion of the Balbina dam resulted a loss of lateral and longitudinal connectivity for the Uatumã River, and the alteration to seedling communities may alter the future landscape of downstream igapó forests.