The impacts of changes in climate are often most readily observed through the effects of extremes in local weather, effects that often propagate through multiple ecosystem levels. Precise effects of any extreme weather event depend not only on the type of event and its timing, but also on the ecosystem affected. Here the cascade of effects following the arrival of an atmospheric river (directed by record-breaking Storm Desmond) across terrestrial, freshwater and coastal zones is quantified, using the Burrishoole system on the Atlantic coast of Ireland as a natural observatory. We used a network of high-frequency in-situ sensors to capture in detail the effects of an unprecedented period of rainfall, high wind speeds and above-average winter air temperatures on catchment and estuarine dynamics. In the main freshwater lake, water clarity decreased and acidity increased during Storm Desmond. Surface heat input, due to a warm and moist above-lake air mass, was rapidly distributed throughout the water column. River discharge into the downstream coastal basin was estimated to be the highest on record (since 1976), increasing the buoyancy flux by an order of magnitude and doubling the water column stratification stability. Entrainment of salt into the outflowing freshwater plume exported resident salt from the inner estuarine basin, resulting in net salt loss. Here, the increased stratification markedly reinforced isolation of the bottom waters, promoting deoxygenation. Measurements of current between the inner estuarine basin and the adjacent coastal waters indicated a 20-fold increase in the volume of seaward flowing low-salinity water, as a result of storm rainfall over the watershed. Storm impacts spanned the full catchment-to-coast continuum and these results provide a glimpse into a potential future for hydrological systems where these severe hydroclimatic events are expected to occur more frequently.