A novel method for the trace analysis of natural and synthetics estrogens, such as estrone (E1), 17beta-estradiol (E2) and 17alpha-ethynylestradiol (EE), in river water sample was developed, which involved stir bar sorptive extraction (SBSE) with in situ derivatization followed by thermal desorption (TD)-gas chromatography-mass spectrometry (GC-MS). The derivatization conditions with acetic acid anhydride and the SBSE conditions such as sample volume and extraction time were investigated. In addition, the single and multi-shot modes in TD were investigated. The detection limits of E1, E2 and EE in river water sample were 0.2, 0.5 and 1 pg ml(-1) (ppt), respectively, in the multi-shot mode using five stir bars. The calibration curves for E1, E2 and EE were linear and had correlation coefficients >0.99. The average recoveries of E1, E2 and EE from all sample volumes were higher than 90% (R.S.D. < 10%) with correction using an added surrogate standard such as estrone-13C4, 17beta-estradiol-13C4 or 17alpha-ethynylestradiol-13C4. This simple, accurate, sensitive and selective analytical method may be applicable to the determination of trace amounts of estrogens in water samples.