We have developed a modelling framework that synthesizes various types of field measurements at different spatial and temporal scales. We used this modelling framework to estimate monthly means and their standard deviations of gross photosynthesis, total ecosystem production, net primary production (NPP) and net ecosystem production (NEP) for eight regions of the Australian continent between 1990 and 1998. Annual mean NPP of the Australian continent varied between 800 and 1100 Mt C yr−1 between 1990 and 1998, with a coefficient of variation that is defined as the ratio of standard deviation and mean between 0.24 and 0.34. The seasonal variation of NPP for the whole continent varied between 50 and 110 Mt C month−1 with two maxima, one in the autumn and another in the spring. NEP was most negative in the winter (a carbon sink) and was most positive (a carbon source) in the summer. However, the coefficient of variation of monthly mean NEP was very large (> 4), and consequently confidence in the predicted net carbon fluxes for any month in the period 1990–1998 for the whole continent was very low. A companion paper will apply atmospheric inverse technique to measurements of CO2 concentration to further constrain the continental carbon cycle and reduce uncertainty in estimated mean monthly carbon fluxes.