North Australian tropical savanna accounts for 12% of the world's total savanna land cover. Accordingly, understanding processes that govern carbon, water and energy exchange within this biome is critical to global carbon and water budgeting. Climate and disturbances drive ecosystem carbon dynamics. Savanna ecosystems of the coastal and sub-coastal of north Australia experience a unique combination of climatic extremes and are in a state of near constant disturbance from fire events (1 in 3 years), storms resulting in windthrow (1 in 5-10 years) and mega-cyclones (1 in 500-1000 years). Critically, these disturbances occur over large areas creating a spatial and temporal mosaic of carbon sources and sinks. We quantify the impact on gross primary productivity (GPP) and fire occurrence from a tropical mega-cyclone, tropical Cyclone Monica (TC Monica), which affected 10 400 km2 of savanna across north Australia, resulting in the mortality and severe structural damage to ∼140 million trees. We estimate a net carbon equivalent emission of 43 Tg of CO 2-e using the moderate resolution imaging spectroradiometer (MODIS) GPP (MOD17A2) to quantify spatial and temporal patterns pre- and post-TC Monica. GPP was suppressed for four years after the event, equivalent to a loss of GPP of 0.5 Tg C over this period. On-ground fuel loads were estimated to potentially release 51.2 Mt CO2-e, equivalent to ∼10% of Australia's accountable greenhouse gas emissions. We present a simple carbon balance to examine the relative importance of frequency versus impact for a number of key disturbance processes such as fire, termite consumption and intense but infrequent mega-cyclones. Our estimates suggested that fire and termite consumption had a larger impact on Net Biome Productivity than infrequent mega-cyclones. We demonstrate the importance of understanding how climate variability and disturbance impacts savanna dynamics in the context of the increasing interest in using savanna landscapes for enhanced carbon sinks in emission offset schemes. © 2013 IOP Publishing Ltd.