Dams alter the natural dynamics of river inflow, disrupting biological processes in downstream ecosystems, as observed in the Guadiana estuary (SW Iberian Peninsula, Europe). Here, significant interannual fluctuations in the densities of jellyfish occur during summer, likely due to changes in winter river discharge. Therefore, this study aimed to quantify the relationship between winter river inflow and the abundance of jellyfish in the Guadiana estuary. In addition, the budding and growth of Aurelia aurita polyps, one of the bloom-forming species present in the estuary, were determined at different combinations of constant temperature and salinity. The response of polyps and ephyrae to short-Term, low-salinity pulses was also quantified. Maximum winter river discharge and maximum abundance of estuarine medusa (bloom indicator) showed a significant negative correlation. Under constant conditions, polyps showed increased mortality when water temperature was higher than 23°C and salinity was lower than 23, and died when exposed to a short-Term, low-salinity pulse (≤3). After exposure to freshets, polyp budding and feeding rates decreased by 69% and 32%, respectively, when salinity reached values as low as 10. Ephyrae died when salinity was lower than 10, and feeding rates decreased by 88% when salinity was 17, compared with full marine conditions. In conclusion, winter freshwater discharge may regulate the strength of estuarine jellyfish blooms, impairing the survival or condition of polyps and ephyrae during late winter or early spring. River basin managers should consider the prescription of freshets to prevent jellyfish blooms from disrupting ecosystem services (e.g. fisheries, tourism).