While substantial attention has been paid to the effects of both global climate oscillations and local meteorological conditions on the interannual variability of ecosystem carbon exchange, the relationship between the interannual variability of synoptic meteorology and ecosystem carbon exchange has not been well studied. Here we use a clustering algorithm to identify a summertime cyclonic precipitation system northwest of the Great Lakes to determine (a) the association at a daily scale between the occurrence of this system and the local meteorology and net ecosystem exchange at three Great Lakes region forested eddy covariance sites and (b) the association between the seasonal prevalence of this system and the summertime net ecosystem exchange of these sites. We find that temperature, in addition to precipitation and cloud cover, is an important explanatory factor for the suppression of net ecosystem productivity that occurs during these cyclonic events in this region. In addition, the prevalence of this cyclonic system can explain a significant proportion of the interannual variability in summertime forest ecosystem exchange in this region. This explanatory power is not due to a simple accumulation of low‐productivity days that cooccur with this meteorological event, but rather a broader association between the frequency of these events and several aspects of prevailing seasonal conditions. This work demonstrates the usefulness of conceptualizing meteorology in terms of synoptic systems for explaining the interannual variability of regional carbon fluxes.