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Free estrogens (estrone, E1; 17 beta-estradiol, 17 beta-E2; estriol, E3; and 17 alpha-ethinylestradiol, EE2), their corresponding sulfate and glucuronide conjugates, and bisphenol A (BPA) were investigated in water and sediments in the Fen River catchment, an arid and semiarid area in northwest China. E1 and BPA were frequently detected in the wet and dry sampling seasons. In addition to the sulfate conjugates, other conjugated estrogens were not detected in water and sediments. The concentrations of these compounds in water generally increased from upstream to downstream. The concentrations in water samples of most sites were higher in the wet season than those in the dry season, but concentrations in sediments of most sites were higher in the dry season than those in the wet season. The distributions of these compounds in sediments were positively correlated with the total organic carbon (TOC) contents of sediments (0.3 < R-2 < 0.6, p < 0.01) and concentrations in water (0.25 < R-2 < 0.50, p < 0.01). In this catchment, E1 was the main contributor to endocrine disrupting risk. The surface water in most of the tributaries and the sewage in the drainage channels were at risk. The pore waters of sediments were at risk at most sampling sites.