1. Substantial amounts of large woody debris have been removed from lowland rivers worldwide. This large woody debris would have been colonised by biofilms and hence would have formed potentially important sites of chemical transformations (particularly carbon uptake) in these riverine environments. It is possible that one of the reasons that allochthonous production appears to be relatively unimportant to metazoan food webs in some river systems is due to the lack of sites suitable for biofilm growth. 2. This paper explores a key aspect underpinning this idea, the kinetics of dissolved organic carbon (DOC) uptake by bacterial biofilms. Laboratory experiments were used to determine the kinetics of uptake of a natural source of DOC in the presence of a range of densities of biofilm-coated surface at different temperatures. Changes in DOC speciation induced by biofilm carbon uptake were examined using 3-dimensional excitation–emission fluorescence spectroscopy with post hoc PARAFAC deconvolution. 3. The first-order rate constant for carbon uptake increased linearly with amount of biofilm present. The rate of uptake is more sensitive to temperature (increasing approximately logarithmically) in the presence than in the absence of added biofilms. Furthermore, it appears that biofilms preferentially remove amino acid-like components from the DOC. 4. Based on these results, we derive a number of testable hypotheses regarding the impact of the reduction of sites of transformation on the functioning of lowland rivers. Specifically, our results suggest that there are both a critical biofilm-coated surface area density and a critical temperature below which carbon uptake in a river reach will be substantially reduced. 5. This implies that both removal of large woody debris and changes in flood seasonality may have altered the potential for incorporation of allochthonous carbon as a basal food resource for riverine food webs.