Large areas of uncompacted cyanobacterial accumulations (or “gyttja”) have been observed in Myall Lake, New South Wales, Australia. To determine whether the cyanobacterial accumulations were assimilated into the local food web, carbon and nitrogen stable isotopes were used to identify the primary food sources of a primary consumer in Myall Lake, the freshwater atyid shrimp Paratya australiensis. Suspended particulate organic matter (POM) and the macrophyte Myriophyllum salsugineum were identified as major dietary sources of P. australiensis. Enriched stable isotope signatures (δ13C and δ15N) of shrimp from gyttja-affected sites, relative to shrimp from unaffected locations, also indicated that P. australiensis were deriving a considerable portion of their dietary carbon and nitrogen requirements from gyttja. Stable isotope mixing models estimated that cyanobacterial accumulations might constitute up to 69% of P. australiensis biomass carbon and nitrogen requirements at gyttja-affected locations. To our knowledge, this is the first study to use stable isotope analysis to trace the assimilation of potentially toxic cyanobacterial accumulations into the trophic pathways of an affected system.