We present a record of extreme spring–summer runoff events for the past 1600 yr preserved in the varved sediments of Lake Mondsee (Austrian Pre-Alps). Combined sediment microfacies analyses and high-resolution micro-X-ray fluorescence element scanning allow us to identify 157 detrital event layers deposited in spring–summer and to discriminate between regional flood and local debris flow deposits. Higher spring–summer flood activity with a mean event recurrence of 3–5 yr occurred in several well-confined multidecadal episodes during the Dark Ages Cold Period and Medieval time (A.D. 450–480, 590–640, 700–750, and 1140–1170) as well as during the early Little Ice Age (LIA; A.D. 1300–1330 and 1480–1520). In contrast, lowest spring–summer flood activity with an event recurrence of only 30–100 yr is observed during the Medieval Climate Anomaly (A.D. 1180–1300) and the coldest interval of the LIA (A.D. 1600–1700). These findings indicate a complex relationship between temperature conditions and extreme hydro-meteorological events and suggest that enhanced summer Mediterranean cyclogenesis triggers large-scale floods in the northeast Alps during climatic transitions. The Lake Mondsee data demonstrate the climatic sensitivity of spring–summer floods and prove the potential of varved sediment records to investigate the impact of changing climate boundary conditions on seasonal flood activity for pre-instrumental time.