Stream food web function is often assessed using carbon stable isotope assessments of the relative contribution of autochthonous and allochthonous sources of organic matter to consumer diets. As a result, variability in source signatures can strongly influence the assessment of carbon flows. To examine the implications of temporal source variability on food web interpretations, benthic algal d13C signatures were measured over 8 weeks in five streams in subtropical Queensland, Australia. All food webs were largely driven by benthic algal carbon; however, substantial week-to-week variation in benthic algal d13C signatures modified the calculated contributions of algae to consumer diets, with differences in autochthonous contributions of up to 11% between weeks. In addition, variable algal signatures led to many occasions in which the d13C signatures of some consumers was beyond the range of available sources, meaning the mixing model analyses did not have a valid solution. Together, these findings suggest that temporal variability in algal d13C signatures can strongly influence the interpretation of carbon flows in stream food webs. Future food web studies should assess the temporal variability of sources prior to sampling consumers, in order to characterise end member signatures and their relevance to consumers at the time of collection.