Despite their size and contribution to the global carbon cycle, we have limited understanding of tropical savannas and their current trajectory with climate change and anthropogenic pressures. Here we examined interannual variability and externally forced long-term changes in carbon and water exchange from a high rainfall savanna site in the seasonal tropics of north Australia. We used an 18-year flux data time series (2001–2019) to detect trends and drivers of fluxes of carbon and water. Significant positive trends in gross primary productivity (GPP, 15.4 g C m2 year−2), ecosystem respiration (Reco, 8.0 g C m2 year−2), net ecosystem productivity (NEE, 7.4 g C m2 year−2) and ecosystem water use efficiency (WUE, 0.0077 g C kg H2O−1 year−1) were computed. There was a weaker, non-significant trend in latent energy exchange (LE, 0.34 W m−2 year−1). Rainfall from a nearby site increased statistically over a 45-year period during the observation period. To examine the dominant drivers of changes in GPP and WUE, we used a random forest approach and a terrestrial biosphere model to conduct an attribution experiment. Radiant energy was the dominant driver of wet season fluxes, whereas soil water content dominated dry season fluxes. The model attribution suggested that [CO2], precipitation and Tair accounting for 90% of the modelled trend in GPP and WUE. Positive trends in fluxes were largest in the dry season implying tree components were a larger contributor than the grassy understorey. Fluxes and environmental drivers were not significant during the wet season, the period when grasses are active. The site is potentially still recovering from a cyclone 45 years ago and regrowth from this event may also be contributing to the observed trends in sequestration, highlighting the need to understand fluxes and their drivers from sub-diurnal to decadal scales.