Conventional simultaneous CNS stable isotope abundance measurements of solid samples usually require high sample amounts, up to 1 mg carbon, to achieve exact analytical results. This rarely used application is often impaired by high C:S element ratios when organic samples are analyzed and problems such as incomplete conversion into sulphur dioxide occur during analysis. We introduce, as a technical innovation, a high sensitivity elemental analyzer coupled to a conventional isotope ratio mass spectrometer, with which CNS-stable isotope ratios can be determined simultaneously in samples with low carbon content (<40 µg C corresponding to ∼100 µg dry weight). The system includes downsized reactors, a temperature program-controlled gas chromatography (GC) column and a cryogenic trap to collect small amounts of sulphur dioxide. This modified application allows for highly sensitive measurements in a fully automated operation with standard deviations better than ±0.47‰ for δ15N and δ34S and ±0.12‰ for δ13C (n = 127). Samples collected from one sampling site in a Baltic fjord within a short time period were measured with the new system to get a first impression of triple stable isotope signatures. The results confirm the potential of using δ34S as a stable isotope tracer in combination with δ15N and δ13C measurements to improve discrimination of food sources in aquatic food webs. Copyright © 2009 John Wiley & Sons, Ltd.