A simple stochastic model is presented to describe the influence of the natural flow regime of the Madre de Dios River (southeastern Peru) on the presence and downstream transportation of catfish larvae (Siluriformes: Pimelodidae), an important migratory species in commercial fisheries in the Peruvian Amazon region. One year of daily river stage records were related to weekly larval catches to determine the association between floods and spawning events, and based on the hydro-climatologic characteristics of Andean-Amazon regions, available long-term historical rainfall records were used to determine the inter-annual variability of floods within the Madre de Dios Basin. Major larval drift occurred during the high water season, specifically in association with stages of over 5 m, which served as an indicator triggering spawning responses of these species, termed a ‘biologically significant event’ (BSE). Timing of these BSEs, estimated from the historical rainfall records, described a uniform distribution during the wet season, and their inter-arrival times were exponentially distributed. These observations provided the basis of the stochastic model describing the likelihood of larvae releases from this headwater region to the lowland Amazon. Copyright © 2011 John Wiley & Sons, Ltd.