This research utilized tower-based eddy covariance to quantify the trends in net ecosystem mass (CO2 and H2O vapor) and energy exchange of important land-cover types of NW Mato Grosso during the March–December 2002 seasonal transition. Measurements were made in a mature transitional (ecotonal) tropical forest near Sinop, Mato Grosso, and a cattle pasture near Cotriguaçú, Mato Grosso, located 500 km WNW of Sinop. Pasture net ecosystem CO2 exchange (NEE) was considerably more variable than the forest NEE over the seasonal transition, and the pasture had significantly higher rates of maximum gross primary production in every season except the dry–wet season transition (September–October). The pasture also had significantly higher rates of whole-ecosystem dark respiration than the forest during the wetter times of the year. Average (±95% CI) rates of total daily NEE during the March–December 2002 measurement period were 26±15 mmol m−2 day−1 for the forest (positive values indicate net CO2 loss by the ecosystem) and −38±26 mmol m−2 day−1 for the pasture. While both ecosystems partitioned more net radiation (Rn) into latent heat flux (Le), the forest had significantly higher rates of Le and lower rates of sensible heat flux (H) than the pasture; a trend that became more extreme during the onset of the dry season. Large differences in pasture and forest mass and energy exchange occurred even though seasonal variations in micrometeorology (air temperature, humidity, and radiation) were relatively similar for both ecosystems. While the short measurement period and lack of spatial replication limit the ability to generalize these results to pasture and forest regions of the Amazon Basin, these results suggest important differences in the magnitude and seasonal variation of NEE and energy partitioning for pasture and transitional tropical forest.