Amazonian ichthyofauna has one of the richest specific diversities on earth. However, life history strategies of most species remain poorly-known owing to logistical difficulties, although this information is essential for species conservation and sustainable fisheries management. An inventory of specific diversity in plankton samples might be an efficient way of studying breeding seasons and breeding localities of fish species, providing their precise taxonomic identification can be ensured. Herein, using barcoding of the cytochrome c oxidase subunit I (COI) gene, species were identified in monthly plankton samples collected in the lower reaches of the Napo, Marañón and Ucayali rivers. A total of 16 species of pimelodid catfish were identified. For the most abundant species, two tendencies were observed, with breeding periods preferentially occurring during rising and high water periods (Brachyplatystoma filamentosum, Pimelodus blochii) or during receding and low water periods (Brachyplatystoma rousseauxii, Brachyplatystoma platynemum, Brachyplatystoma vaillantii, Hypophthalmus edentatus, Hypophthalmus marginatus). For all of these species except for B. rousseauxii, this is new information for the Peruvian Amazon. Their reproductive behaviours are discussed in term of adaptive strategies to environmental conditions, where hydrological cycles play essential roles in resource accessibility and dispersal capabilities.