Abstract The occurrence and fate of fourteen androgens, four estrogens, five glucocorticoids and five progestagens were investigated by rapid resolution liquid chromatography-tandem mass spectrometry (RRLC-MS/MS) in a typical swine farm with lagoon waste disposal systems, in south China. Nineteen, 22 and 8 of 28 steroids were detected at concentrations ranging from 2.2 ± 0.1 ng/g (androsta-1,4-diene-3,17-dione) to 14,400 ± 394 ng/g (progesterone) in the feces samples, from 6.1 ± 2.3 ng/L (17β-boldenone) to 10,800 ± 3190 ng/L (norgestrel) in the flush water samples, and from 5.0 ± 0.2 ng/g (progesterone) to 225 ± 79.4 ng/g (5α-dihydrotestosterone) in the suspended particles, respectively. By comparing the types and concentrations of steroids in different treatment stages of the lagoon systems, it demonstrated that the lagoon systems used in the farm were not effective method to reduce various steroids in wastewater. Among the thirteen synthetic steroids detected in the swine feces and flush water, only seven (methyl testosterone, 17α-trenbolone, 17β-trenbolone, 17α-ethynyl estradiol, dexamethasone, medroxyprogesterone, and norgestrel) were regarded as the parent/metabolite compounds of animal exogenous usage. According to the estimated masses of steroids from feces and flush water, the excretion of steroids for sows were mainly from feces, but for piglets or barrows, most excreted steroids were through flush water rather than feces. The total daily excreted masses of androgens, estrogens, glucocortcoids and progestagens in the sow feces were in the range of 90.7–6310 μg/d, which were up to a thousand fold of those in the feces of other growth stages indicating that the proportion of sow number in the swine farm directly influenced the total excretion mass of steroids. In addition, two natural steroids 4-androstene-3,17-dione and progesterone were worth notice due to their relatively high concentrations per sow excretion, 277 μg/d and 6380 μg/d, respectively, which are approximately equivalent to the daily excretion of 100 persons. Some steroids were also detected in the well water, vegetable field and receiving stream, and may pose potential high risks to some sensitive organisms in the receiving environment.