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The North Atlantic Storm Track acts as a conveyor belt for extratropical cyclones that frequently deliver high winds and rainfall to northwest European shelf seas. Storms are primarily considered detrimental to shelf sea stratification due to wind-driven mixing countering thermal buoyancy, but their impact on shelf scale stratification cycles remains poorly understood. Here, we show that storms trigger stratification through enhanced surface buoyancy from rainfall. A multidecadal model confirms that rainfall contributed to triggering seasonal stratification 88% of the time from 1982 to 2015. Stratification could be further modulated by large-scale climate oscillations, such as the Atlantic Multidecadal Variability (AMV), with stratification onset dates being twice as variable during a positive AMV phase than a negative one. Further insights into how changing storm activity will impact shelf seas are discussed beyond the current view of increasing wind-driven mixing, with significant implications for marine productivity and ecosystem function.