Results/Conclusions The data-model fusion procedure skillfully reproduced the majority of diurnal variation in NEE for all sampling periods. Both sites exhibited a maximum in diurnal assimilation occurring on average between 0.5 to 4 hours before solar noon; the timing of peak assimilation was closely related to maximum daily vapor pressure deficit. The woodland site had consistently higher assimilation rates, lower seasonal variability, and a larger diurnal assimilation hysteresis compared to the grassland site. We examined the causes of this variation using a new state factor model analysis that partitioned ecosystem physiologic variation into four factors: meteorology, water supply, physiology, and leaf area. The largest proportion of variation in assimilation and net exchanges was primarily associated with physiological differences. When comparing the two community types, the woodland showed a greater sensitivity than the grassland to water supply, while the grassland showed a greater sensitivity to leaf area than the woodland. The coupling of ecophysiological theory with sub-hourly eddy-covariance data in the context of a state factor model provided an important approach for understanding ecological responses to environmental variability.