• Results from a multi-year carbon and water flux analysis over sub-tropical coastal ecosystems are presented. • Evaporation found to dominate over transpiration in native ecosystems. • Availability of atmospheric and/or soil water was the strongest influence on variations in ecosystem carbon exchange. • Gross Ecosystem Production of a coastal sub-tropical wetland found to be similar to tropical forests. Coastal wetland environments are an important sub-tropical ecosystem and a significant sink of carbon dioxide. They are under threat globally from coastal development, climate change, and sea level rise. Here we present eddy covariance measurements of carbon and water fluxes over three contrasting sub-tropical coastal ecosystems in eastern Australia: a wetland, an intermittently inundated swamp, and a commercial pine plantation. The aim is to quantify net ecosystem exchange and evapotranspiration to identify the meteorological and environmental factors that control carbon and water flux in these ecosystems. Results show that annual net ecosystem production ranged from 396 and 514 gC m-2 year-1 at the wetland, 571 and 694 gC m-2 year-1 at the pine plantation, and -74 and 108 gC m-2 year-1 at the swamp. In addition to photosynthetically available radiation and temperature, the strongest drivers of carbon flux were volumetric water content, vapour pressure deficit, and evapotranspiration at the wetland and swamp; at the swamp, leaf area index was also strongly correlated with carbon flux. In contrast, at the pine plantation, in addition to photosynthetically available radiation and temperature, only vapour pressure deficit had a strong correlation to carbon flux, with much weaker contribution from volumetric water content and leaf area index, and negligible correlation with evapotranspiration. Annual gross ecosystem production of the wetland site (2664–2739 gC m-2 year-1) was similar to those of tropical forests, while the pine plantation was the most effective at carbon capture from the atmosphere. Results provide valuable insight to these ecosystems and their water/carbon exchanges with the atmosphere, from which future change in response to climate change and land use change can be quantified. [ABSTRACT FROM AUTHOR]