The magnitude of the terrestrial carbon (C) sink may be overestimated globally due to the difficulty of accounting for all C losses across heterogeneous landscapes. More complete assessments of net landscape C balances (NLCB) are needed that integrate both emissions by fire and transfer to aquatic systems, two key loss pathways of terrestrial C. These pathways can be particularly significant in the wet–dry tropics, where fire plays a fundamental part in ecosystems and where intense rainfall and seasonal flooding can result in considerable aquatic C export (ΣFaq). Here, we determined the NLCB of a lowland catchment (~140 km2) in tropical Australia over 2 years by evaluating net terrestrial productivity (NEP), fire-related C emissions and ΣFaq (comprising both downstream transport and gaseous evasion) for the two main landscape components, that is, savanna woodland and seasonal wetlands. We found that the catchment was a large C sink (NLCB 334 Mg C km−2 year−1), and that savanna and wetland areas contributed 84% and 16% to this sink, respectively. Annually, fire emissions (−56 Mg C km−2 year−1) and ΣFaq (−28 Mg C km−2 year−1) reduced NEP by 13% and 7%, respectively. Savanna burning shifted the catchment to a net C source for several months during the dry season, while ΣFaq significantly offset NEP during the wet season, with a disproportionate contribution by single major monsoonal events—up to 39% of annual ΣFaq was exported in one event. We hypothesize that wetter and hotter conditions in the wet–dry tropics in the future will increase ΣFaq and fire emissions, potentially further reducing the current C sink in the region. More long-term studies are needed to upscale this first NLCB estimate to less productive, yet hydrologically dynamic regions of the wet–dry tropics where our result indicating a significant C sink may not hold.