Central Europe has experienced a sequence of unprecedented summer droughts since 2015, which had considerable effects on the functioning and productivity of natural and agricultural systems. Placing these recent extremes in a long-term context of natural climate variability is, however, constrained by the limited length of observational records. Here, we use tree-ring stable oxygen and carbon isotopes to develop annually resolved reconstructions of growing season temperature and summer moisture variability for central Europe during the past 2000 years. Both records are independently interpolated across the southern Czech Republic and northeastern Austria to produce explicit estimates of the optimum agroclimatic zones, based on modern references of climatic forcing. Historical documentation of agricultural productivity and climate variability since 1090 CE provides strong quantitative verification of our new reconstructions. Our isotope records not only contain clear expressions of the medieval (920–1000 CE) and Renaissance (early sixteenth century) droughts, but also the relative influence of temperature and moisture on hydroclimatic conditions during the first millennium (including previously reported pluvials during the early third, fifth, and seventh centuries of the Common Era). We conclude that Czech agricultural production has experienced significant extremes over the past 2000 years, which includes periods for which there are no modern analogs.