ABSTRACTEphemeral macroalgal blooms have been increasing in frequency and abundance worldwide. We investigated the variability of drift macroalgae abundance in a shallow bay of the Patos Lagoon Estuary (PLE) in southern Brazil to determine the influence of climate and hydrology on the onset and magnitude of blooms. During the study period (January 2004 to May 2007), three growth cycles were observed and differed in timing, magnitude and persistence. Macroalgal biomass (mostly Ulva species) varied annually and interannually (3 g DW m−2 to 432.7 g DW m−2), peaking during the spring and summer. On an annual scale, macroalgal blooms occurred after reductions in freshwater discharge and associated decreases in water level and increases in salinity and retention. These hydrological parameters were influenced by precipitation which, in turn, is affected by the El Niño Southern Oscillation. On an interannual scale, the largest bloom was observed during a weak-moderate El Niño year. No direct relationship was found between biomass peaks and water nutrient concentrations, but tissue nitrogen content indicated no nitrogen limitation. However, a trend of increasing phosphorus concentration (resulting in decreased DIN:DIP ratios) may be associated with the largest bloom observed. Under favourable hydrological conditions for growth, wind action affected the algal transport in shallow areas, thereby controlling the magnitude and persistence of the blooms. The macroalgal abundance found in the PLE was comparable to that found in temperate eutrophic lagoons, highlighting an algal-dominated period triggered by the combined effects of climate and hydrological factors in a post-El Niño period.