In the paper, a modified method for elemental sulfur (S) determining using gas chromatography coupled with mass spectrometry (GC-MS) is proposed with estimation of selected validation parameters. The aim of this work was a review of problems associated with the determination of S and selection of the most optimal conditions for S analysis with GC-MS. The presented studies have shown that the temperature of the injector and the chromatographic column during S determination should not exceed 180 °C. At temperatures over 180 °C, the sulfur S is decomposed to the other sulfur species such as S, S, S, S, and S. During decreasing injector and column temperature below 180 °C the chromatographic peak eluted as S is badly extended and asymmetric. To minimize the problems of S decomposition to other sulfur species during chromatographic process also other parameters of the GC-MS have been selected. In order to apply the proposed method for real sediments samples, determination of sulfur S in bottom sediments, collected in the Gulf of Gdansk (southern Baltic Sea), has been performed. The concentration of S fell in the range from below the limit of detection to 0.1432 ± 0.0095 mg/g d.w. The research has also shown that addition of approx. 200 mg of activated copper is effective for removing sulfur from bottom sediment extracts.