Density-dependent regulation is a necessary process for the long-term persistence of populations. Nevertheless, ecologists still debate whether floodplain fish populations are subject to density-dependent dynamics or mostly regulated by the density-independent seasonal flooding. We surveyed Jewel tetra (Hyphessonbrycon eques) populations during 4 years in the floodplain lagoons of the Cuiaba River (Brazil) in order to determine if recruitment, growth, and survival are subject to density-dependent effects. We showed that population dynamics of this species are influenced by the seasonal drought, which affects the various life stages of the cohort in different ways. The flood had positive effects on the strength of recruitment, and indirectly affected the probability of survival of recruits during the following dry season as well as on the extinction probability of local populations. Additionally, by facilitating the dispersal of pre-larvae and juvenile recruits, it enables the re-establishment of locally extinct populations during the preceding dry season. Therefore, flooding is essential for the persistence of the species at the regional scale. On the other hand, the limiting conditions during the dry season cause high mortality rates among juveniles. More importantly, the mortality during the dry season is density-dependent and causes changes in population size structure and extinction of local populations, which will affect recruitment in the following year. Our results change the traditional belief that flood alone control population dynamics of fish dwelling in floodplains of larger rivers but a longer survey is required to better understand the effects of drought.