The Mondego estuary (Portugal) experienced profound structural and functional modifications due to eutrophication, which was exacerbated by consecutive weather extremes that compromised a previous restoration project. This work explores multiple climate impacts on macrobenthic communities' structure and functioning and its implications on ecosystem's recovery. Floods and heat waves had a stronger negative effect on macrobenthic assemblages than the droughts, imposing a total abundance decline. Contrarily, biomass was not so affected by climate events, being stable and even increased in a mudflat area, where seagrass is re-colonizing. Bivalves and oligochaetes decreased with the flooding episodes, likewise subsurface-deposit feeders and suspension feeders, while crustaceans were particularly sensitive to heat waves. Species richness declined with the floods and heat waves, whilst evenness increased in sandflat area, constituting a positive sign towards recovery. Succession of different climate extremes affected ecosystem structure and functioning, delaying its recovery with possible consequent effects at higher trophic levels.