Utilising newly available instrumentation, the carbon balance in two small tropical catchments was measured during two discharge events at high temporal resolution. Catchments share similar climatic conditions, but differ in land use with one draining a pristine rainforest catchment, the other a fully cleared and cultivated catchment. The necessity of high resolution sampling in small catchments was illustrated in each catchment, where significant chemical changes occurred in the space of a few hours or less. Dissolved and particulate carbon transport dominated carbon export from the rainforest catchment during high flow, but was surpassed by degassing of CO2 less than 4 h after the discharge peak. In contrast, particulate organic carbon dominated export from the cleared catchment, in all flow conditions with CO2 evasion accounting for 5–23% of total carbon flux. Stable isotopes of dissolved inorganic carbon (DIC) in the ephemeral rainforest catchment decreased quickly from ~1.5 ‰ to ~ −16 ‰ in 5 h from the flood beginning. A two-point mixing model revealed that in the initial pulse, over 90% of the DIC was of rainwater origin, decreasing to below 30% in low flow. In the cultivated catchment, δ13CDIC values varied significantly less (−11.0 to −12.2 ‰) but revealed a complex interaction between surface runoff and groundwater sources, with groundwater DIC becoming proportionally more important in high flow, due to activation of macropores downstream. This work adds to an increasing body of work that recognises the importance of rapid, short-lived hydrological events in low-order catchments to global carbon dynamics. Copyright © 2013 John Wiley & Sons, Ltd.