Abstract This study assessed the phenology and functional structure of parental stocks of fish larvae, and evaluated how the species modulate their reproductive activities as a function of natural hydrological regimes in the lower Amazon River, Brazil. Larvae were collected using conical plankton nets monthly over two hydrological cycles between January and December 2013, and between May 2017 and April 2018. The collections were conducted around an alluvial island located near the municipality of Santarém, Pará, Brazil. After identification, individuals were classified into four functional groups (e.g., life‐history strategy, feeding habits, type of migration, and swimming‐performance/microhabitat‐use in the water column) based on species traits. The relationships between seasonal hydrology, environmental variables and larval assemblage structure were evaluated using multivariate analyses. A total of 31,347 fish larvae were collected, from nine taxonomic orders, 26 families, 40 genera and 53 species. The larval assemblages showed highly variable taxonomic and functional composition between different phases of the hydrological cycle (rising water, high water, receding water and low water) and were strongly influenced by environmental variables. Fish reproductive phenology in the lower Amazon is complex and distributed among the hydrological phases. The different ecological characteristics allow the species to withstand specific environmental conditions during each phase. Changes in the structure of larval assemblages indicate that hydrological variability is a key ecological factor influencing the reproductive dynamics of fish and reflects adaptive strategies used to reduce interspecific competition for space and food, maximising recruitment. The variation of fish reproduction across the hydrological cycle that we observed is a result of different ecological characteristics enabling species and functional groups to adapt to environmental conditions of each phase.