We evaluated the structure of the ichthyoplanktonic assemblage (taxonomic composition, abundance, developmental stages, and relationship with local environmental variables) in marginal lagoons located in the clearwater Tapajós and Trombetas rivers, Amazon Basin, Brazil during periods of high water (rising waters and flooding). Samples were collected by means of horizontal drags in the subsurface of the water with a plankton net (300 µm mesh). Sorting, counting, identification of biological material, and classification of embryonic and larval stages were performed under a stereoscopic microscope. A total of 122 eggs and 2,813 fish larvae were captured and distributed in nine orders, 18 families, 20 genera, and 26 species. Of these, more than 75% are considered sedentary or short-distance migrants and more than 50% are of commercial interest. The results revealed fluctuating patterns of abundance and species composition between the lagoons of the two rivers. The ichthyoplankton community in the lagoons consisted mainly of larvae of native pelagic fish belonging to the Engraulidae family and larvae of benthic fish such as Eleotridae, making up more than 85% of the individuals captured in the study area. In addition to these two groups, some larvae of piranha species (Pygocentrus nattereri) stood out due to their high densities in the Tapajós river lagoons and croaker larvae (Plagioscion spp.) in the Trombetas river lagoons. The highest larval densities were recorded during the night with significant variations recorded in species composition. The presence of all stages of larval development indicates that these biotopes enable growth and are essential for the biological recruitment of fish species in the region. The ichthyoplankton showed a low correlation with the limnological variables, however, the patterns of abundance and composition of fish larval assemblages in the lagoons of the Tapajós and Trombetas rivers were preliminarily elucidated, although additional work is needed to assess the effects on survival and recruitment