Carbon stable isotope ratios were determined in dominant biotic components of pelagic and littoral systems in Alchichica crater-lake. Results showed that carbon signatures were significantly different between both systems. The pelagic environment was more depleted (−26.15 to −15.14 per mille) than the littoral zone (−21.03 to −17.91 per mille). The potential source end-point in the simplified pelagic community was established to be diatomaceous phytoplankton; its predicted value was −21.7 per mille. There is a clear evidence thatNodularia does not sustain the pelagic food chain. In contrast, the highly diverse littoral community was sustained by epiphytes. No allochthonous sources seemed to influence this food web.13C enrichment was observed along the components of both systems with fractionations of 0.8 to 1.4 per mille. The contribution of the seagrassRuppia maritima is probably associated with the detritus pathway. Carbon source partitioning between both systems was not recorded. The δ13C in Alchichica crater-lake was more enriched than in other saline lakes and could be attributed to different salinity and CO2 concentrations among lakes.