Carbon and nitrogen stable isotope ratios (13C and 15N) and trophic level (TL) estimates based on stomach content analysis and published data were used to assess the contribution of autotrophic sources to 55 consumers in an intertidal mangrove creek of the Curuçás estuary, northern Brazil. Primary producers showed δ13C signatures ranging between −29.2 and −19.5‰ and δ15N from 3.0 to 6.3‰. The wide range of the isotopic composition of carbon of consumers (−28.6 to −17.1‰) indicated that different autotrophic sources are important in the intertidal mangrove food webs. Food web segregation structures the ecosystem into three relatively distinct food webs: (i) mangrove food web, where vascular plants contribute directly or indirectly via POM to the most 13C-depleted consumers (e.g. Ucides cordatus and zooplanktivorous food chains); (ii) algal food web, where benthic algae are eaten directly by consumers (e.g. Uca maracoani, mullets, polychaetes, several fishes); (iii) mixed food web where the consumers use the carbon from different primary sources (mainly benthivorous fishes). An IsoError mixing model was used to determine the contributions of primary sources to consumers, based on δ13C values. Model outputs were very sensitive to the magnitude of trophic isotope fractionation and to the variability in 13C data. Nevertheless, the simplification of the system by a priori aggregation of primary producers allowed interpretable results for several taxa, revealing the segregation into different food webs.