The relationship between the frequency of River Ammer floods (southern Germany) and atmospheric circulation variability is investigated based on observational Ammer River discharge data back to 1926 and a flood layer time series from varved sediments of the downstream Lake Ammer for the pre-instrumental period back to 1766. A composite analysis reveals that, at synoptic timescales, observed River Ammer floods are associated with enhanced moisture transport from the Atlantic Ocean and the Mediterranean towards the Ammer region, a pronounced trough over western Europe as well as enhanced potential vorticity at upper levels. We argue that this synoptic-scale configuration can trigger heavy precipitation and floods in the Ammer region. Interannual to multidecadal increases in flood frequency, as detected in the instrumental discharge record, are associated with a wave train pattern extending from the North Atlantic to western Asia, with a prominent negative center over western Europe. A similar atmospheric circulation pattern is associated with increases in flood layer frequency in the Lake Ammer sediment record during the pre-instrumental period. We argue that the complete flood layer time series from Lake Ammer sediments covering the last 5500 years contains information about atmospheric circulation variability on interannual to millennial timescales.