Estrogens have been widely detected in water and might pose a potential threat to the aquatic ecosystem. However, little information is available about the occurrence, multi-phase fate and potential risks of estrogens in Hanjiang River (HR). In this work, the concentration, multi-phase distribution and risk assessment of eight estrogens were studied by investigating surface water and sediment samples from HR during two seasons. These samples were analyzed using the solid-phase extraction (SPE) and liquid chromatography-mass spectrometry (LC-MS). The concentrations of eight estrogens were 4.5–111 ng/l in surface water and 1.7–113 ng/g dry weight in sediments. 4-nonylphenol (NP) was the predominant estrogen in both water and sediments. The estrogens showed significantly spatial variability, with the highest average concentration in the lower section of HR (p < 0.01, F > 12.21). Meanwhile, NP, 17α-estradiol (αE2), Bisphenol A (BPA) and 4-tertoctyphenol (OP) in surface water exhibited higher concentrations in summer than in winter (p < 0.05, F > 4.62). The sediment-water partition coefficients of estrogens suggested that these compounds partitioned more to particulate phase. Risk assessment indicated that estriol (E3) was the main contributor to the total estradiol equivalent concentration. Moreover, estrogen mixtures could pose high ecological risks to aquatic organisms in surface water. Overall, estrogens are ubiquitous in HR, and their potential ecological risks should not be neglected.