A major role of the National Center for Atmospheric Research (NCAR) Electra aircraft during the Boreal Ecosystem-Atmosphere Study (BOREAS) was to measure fluxes of momentum, sensible and latent heat, carbon dioxide, and ozone on a transect that crossed the entire boreal forest biome. The observations spanned the growing season (late May to mid-September 1994) and extended the fluxes obtained in two intensive study areas to larger spatial scales to help provide a data set that is useful for comparison with and validation of large-scale models and satellite retrievals. We found the deciduous forests to be more photosynthetically active than nearby coniferous forests. Coniferous forest fluxes across the transect from the BOREAS southern to northern study areas show no apparent spatial trend, though smaller-scale variability is large. The fluxes make a smooth transition from the BOREAS northern study area to the subarctic tundra. Typical midsummer, midday, large-scale net ecosystem exchanges of carbon dioxide were about −10 μmol m−2 s−1 for primarily deciduous forests, about −6 μmol m−2 s−1 for the primarily coniferous regions between and including the two BOREAS study areas, and about −2 μmol m−2 s−1 for the subarctic tundra. The first two values are similar to those observed by flux towers in the region. Throughout the boreal forest the fluxes are influenced by the presence of lakes. Lake fraction is found to be a dominant source of variability in the fluxes observed along the transect. Lakes are also found to be large sinks of available radiant energy. Regional ground storage of heat is estimated to be about 30% of the net radiation over the forest, and 40% over the subarctic tundra, largely due to the presence of lakes.