The role and quantitative importance of free-living nematodes in marine and estuarine soft sediments remain enigmatic for lack of empirical evidence on the feeding habits and trophic position of most nematode species. Here we use natural abundances of carbon and nitrogen stable isotopes of some abundant nematode species/genera from estuarine intertidal sediments to assess their trophic level and major food sources. In all stations, δ15N of different dominant nematode species/genera spanned a range of 3.6 to 6.3 ppt, indicating that at least two trophic levels were represented. The large nematodes Enoplus brevis, Enoploides longispiculosus and Adoncholaimus fuscus consistently had high δ15N, in line with mouth-morphology based predictions and empirical evidence on their predacious feeding modes. Daptonema sp., Metachromadora remanei, Praeacanthonchus punctatus and ‘Chromadoridae’ (dominated by Ptycholaimellus ponticus) had comparatively lower δ15N, and δ13C suggesting that microphytobenthos (MPB) is their major carbon source, although freshly sedimented particulate organic matter may also contribute to their nutrition in silty sediments. The trophic position of Sphaerolaimus sp., a genus with documented predacious feeding mode, was ambiguous. Ascolaimus elongatus had δ15N signatures indicating a predacious ecology, which is at variance with expectations from existing feeding type classifications. Our study shows that—despite limitations imposed by the biomass requirements for EA-IRMS (elemental analyser—isotope ratio mass spectrometry)—natural isotope abundances of carbon and nitrogen are powerful tools to unravel trophic structure within nematode communities. At the same time, the prominence of different trophic levels results in a large span of δ15N, largely invalidating the use of nitrogen isotope abundances to assess food sources and trophic level of whole nematode communities.