Coastal areas are typically subjected to a range of stressors, but they now face the additional stressor of climate change, manifested in part by an increased intensity and frequency of extreme weather events. Thus, the Mondego estuary (Portugal) has experienced organic enrichment (eutrophication) issues and these are potentially exacerbated by extreme weather events (floods, droughts and heat waves). In this paper, we explore the impact of interactions of these different stressors on the ecology of the system, specifically on the two key components, the seagrass Zostera noltii and the mud snail Hydrobia ulvae. Extreme events affected different components of the estuarine ecosystem (primary producers and macrofauna) differently. Whilst the floods directly impacted on H. ulvae, by wiping out part of its population, they did not directly affect the biomass of Z. noltii. In contrast, drought events, through their effects on salinity, directly impacted the biomass of Zostera, which had knock-on effects on the dynamics of H. ulvae. We conclude that over the period when the estuary experienced eutrophication, extreme weather events contributed to the overall degradation of the estuary, while during the recovery phase following the introduction of a management programme, those extreme weather episodes delayed the recovery process significantly.