Algae and terrestrial organic matter are the basal resources for river food webs. Once organic carbon is fixed within or delivered to a stream, it can be sequestered in sediments, assimilated into microbial or animal biomass, respired as CO2, or transported downstream. We have become increasingly good at measuring the losses of organic C from rivers through CO2 evasion and via DIC and DOC export. Yet the organic matter retained (the amount of fixed carbon contributing to river food webs) has received much less attention. This retention represents a small fraction of carbon fluxes through reaches, yet it is this fraction that represents the food available to freshwater organisms, and changes in the distribution of carbon fixation, retention and assimilation will thus have important implications for freshwater biodiversity. We have developed a synthetic river network meta-ecosystem model to couple simple models of stream metabolism and litter transport and transformation with the population dynamics of stream invertebrates. The framework allowed us to control for light availability, vegetation cover and phenology, temperature and hydrologic regimes. We performed a set of simple in silico experiments to examine how two climate-change-related drivers are likely to alter the distribution of basal resources and primary consumers throughout a river network. Rising temperatures speed the microbial decomposition of organic matter stocks and the respiratory costs for all organisms, while higher peak flows displace standing stocks of organic matter and algal biomass downstream. Our exploratory model suggests that these two common climate change trajectories should reduce the residence time of fixed carbon throughout river networks, deplete food availability in headwaters, and reduce biomass residence times. Our model results suggest that these common climate drivers will deplete freshwater energy supply and animal abundance in low order streams, leading to significant declines at network scales