Lakes are an important source and sink of atmospheric CO2, and thus are a vital component of the global carbon cycle. However, with scarce data on potentially important subtropical and tropical areas for whole continents such as Australia, the magnitude of large-scale lake CO2 emissions is unclear. This study presents spatiotemporal changes of dissolved inorganic carbon and water - to - air interface CO2 flux in the two of Australia's largest connected, yet geomorphically different freshwater lakes (Lake Alexandrina and Lake Albert, South Australia), during drought (2007 to September-2010) and post-drought (October 2010 to 2013). Lake levels in the extreme drought were on average approximately 1m lower than long-term average (0.71m AHD). Drought was associated with an increase in the concentrations of dissolved inorganic species, organic carbon, nitrogen, Chl-a and major ions, as well as water acidification as a consequence of acid sulfate soil (ASS) exposure, and hence, had profound effects on lake pCO2 concentrations. Lakes Alexandrina and Albert were a source of CO2 to the atmosphere during the drought period, with efflux ranging from 0.3 to 7.0mmol/m2/d. The lake air-water CO2 flux was negative in the post-drought, ranging between -16.4 and 0.9mmol/m2/d. The average annual CO2 emission was estimated at 615.5×106mol CO2/y during the drought period. These calculated emission rates are in the lower range for lakes, despite the potential for drought conditions that shift the lakes from sink to net source for atmospheric CO2. These observations have significant implications in the context of predicted increasing frequency and intensity of drought as a result of climate change. Further information on the spatial and temporal variability in CO2 flux from Australian lakes is urgently warranted to revise the global carbon budget for lakes.