The growth rate of atmospheric CO2 exhibits large temporal variation that is largely determined by year-to-year fluctuations in land–atmosphere CO2 fluxes. This land–atmosphere CO2-flux is driven by large-scale biomass burning and variation in net ecosystem exchange (NEE). Between- and within years, NEE varies due to fluctuations in climate. Studies on climatic influences on inter- and intra-annual variability in gross photosynthesis (GPP) and net carbon uptake in terrestrial ecosystems have shown conflicting results. These conflicts are in part related to differences in methodology and in part to the limited duration of some studies. Here, we introduce an observation-driven methodology that provides insight into the dependence of anomalies in CO2 fluxes on climatic conditions. The methodology was applied on fluxes from a boreal and two temperate pine forests. Annual anomalies in NEE were dominated by anomalies in GPP, which in turn were correlated with incident radiation and vapor pressure deficit (VPD). At all three sites positive anomalies in NEE (a reduced uptake or a stronger source than the daily sites specific long-term average) were observed on summer days characterized by low incident radiation, low VPD and high precipitation. Negative anomalies in NEE occurred mainly on summer days characterized by blue skies and mild temperatures. Our study clearly highlighted the need to use weather patterns rather than single climatic variables to understand anomalous CO2 fluxes. Temperature generally showed little direct effect on anomalies in NEE but became important when the mean daily air temperature exceeded 23 °C. On such days GPP decreased likely because VPD exceeded 2.0 kPa, inhibiting photosynthetic uptake. However, while GPP decreased, the high temperature stimulated respiration, resulting in positive anomalies in NEE. Climatic extremes in summer were more frequent and severe in the South than in the North, and had larger effects in the South because the criteria to inhibit photosynthesis are more often met.