This study has demonstrated that geomorphic complexity has a significant effect upon the spatial distribution of carbon in the Lower Balonne River Floodplain, south-west Queensland. Three scales of variability were found. At the macro-scale, total carbon storage was influenced by the effect of a low-angle alluvial fan upon which the floodplain has developed. Total carbon storage in the floodplains of different process zones or rivers (at the meso-scale) was influenced by river-channel planform and particle size. At the micro-scale, geomorphic units affected both total carbon storage and dissolved organic carbon release from floodplain sediments. Total nitrogen storage was also strongly affected by geomorphic units, and displayed a similar distribution to that of carbon, however total phosphorus storage did not vary significantly. There is potential for such variability to impact upon riverine ecosystem processes that are based upon the supply of carbon from the floodplain during floods. Moreover, the significance of floodplain geomorphic complexity demonstrated in this study contrasts with the hydrological and biological focus of current ecological concepts and research. The spatial variation in carbon and nutrient storage and supply found in the Lower Balonne River Floodplain demonstrates the necessity of understanding the geomorphology of river-floodplain systems, in order to predict variation in ecosystem processes. Floodplain geomorphic complexity may be more important to ecosystem functioning, and for water and land management, than previously assumed.