Over the past decade, increasing evidence has shown a prevalence of anoxic conditions and contributions of methane-derived carbon to freshwater food webs, highlighting the potential for methanotrophy and chemoautotrophy to occur. However, δ13C values are still commonly interpreted under the assumption that all potential basal carbon sources are photosynthetic. Methanotrophy and chemoautotrophy can provide non-photosynthetic carbon sources that are sometimes cryptic, or present at such low concentrations that they might not provide an obvious carbon source, especially in rivers which are typically conceptualized as well-oxygenated. At most, chemoautotrophy and methanotrophy might be important, yet overlooked, carbon sources, and at least, even a small amount of these isotopically lighter contributions could complicate assessments of basal carbon sources to river food webs. Even a 1% contribution of methane-derived carbon to consumer biomass could cause 30% error in estimates of allochthony. Stream consumer biomass has included substantial contributions of non-photosynthetic carbon in habitats such as chalk streams, hyporheic zones, backwater pools, and even floodplains of glacial rivers. Herein I review the spatiotemporal distribution of stream conditions conducive to the production and potential consumption of cryptic carbon resources. I argue for a nuanced interpretation of carbon isotope values that explicitly considers three assumptions: representation of dietary end members using bulk sampling, estimation of fractionation rates associated with microbial oxidation reactions, and the decision of whether or not to include proxies for the heavily fractionated biomass of chemoautotrophs and methanotrophs. I suggest that these assumptions be explicitly considered in food web studies conducted in low-gradient, warmer, organic matter-rich, or spring-fed streams which are those which most commonly have the highest methane concentrations, and thus high probabilities of cryptic carbon production. In accounting for cryptic carbon sources, stream food web studies could consider the biogeochemical complexity that is possible in these heterogenous environments, and obtain a more comprehensive understanding of the energy sources that sustain stream consumers.