Lake sediments are increasingly explored as reliable paleoflood archives. In addition to established flood proxies including detrital layer thickness, chemical composition, and grain size, we explore stable oxygen and carbon isotope data as paleoflood proxies for lakes in catchments with carbonate bedrock geology. In a case study from Lake Mondsee (Austria), we integrate high-resolution sediment trapping at a proximal and a distal location and stable isotope analyses of varved lake sediments to investigate flood-triggered detrital sediment flux. First, we demonstrate a relation between runoff, detrital sediment flux, and isotope values in the sediment trap record covering the period 2011–2013 CE including 22 events with daily (hourly) peak runoff ranging from 10 (24) m3 s−1 to 79 (110) m3 s−1. The three- to ten-fold lower flood-triggered detrital sediment deposition in the distal trap is well reflected by attenuated peaks in the stable isotope values of trapped sediments. Next, we show that all nine flood-triggered detrital layers deposited in a sediment record from 1988 to 2013 have elevated isotope values compared with endogenic calcite. In addition, even two runoff events that did not cause the deposition of visible detrital layers are distinguished by higher isotope values. Empirical thresholds in the isotope data allow estimation of magnitudes of the majority of floods, although in some cases flood magnitudes are overestimated because local effects can result in too-high isotope values. Hence we present a proof of concept for stable isotopes as reliable tool for reconstructing flood frequency and, although with some limitations, even for flood magnitudes.