Abstract –  River–floodplain systems present intense temporal variations in physical, chemical and biological factors. These variations are closely related to alterations in water levels, which have been attributed to the flood pulse. As several species are strictly related to the flood pulse to fulfil their life cycle, the pulse may be seen as a dispersal mechanism of species onto a floodplain. In this study, we determine how dam construction influenced the persistence of Prochilodus lineatus population, a large migratory fish species from the upper Paraná River floodplain. Data used were collected in two distinct periods, from April 1992 to March 1993 and from January 1999 to December 2001. Fish were collected using seining nets in six (monthly in the first period) and seven (quarterly in the second period) isolated lagoons. The fraction of occupied lagoons was high in the first period (higher than 0.65), when flood was intense. However, in the second period, when the flood pulse did not happen or was short, the fraction of occupied lagoons sharply decreased over time (from 0.85 to 0.22). For the first period, no model fitted to data, but for the second period, a negative linear model (named drought‐dependent model) presented good fit (r² = 0.97). Therefore, it is possible to infer that long and intense flood pulses are important to maintain the persistence of P. lineatus populations in the floodplain. The artificial control of water levels prompted by dams disrupts this dynamic, reducing persistence to critical levels.