The estrogen receptor alpha (ERα) plays an important role in male reproduction and fertility. Its activity is modulated by phosphorylation of multiple amino acid residues. The ERα phosphorylated at serine 305 (S305) in human cells (homologous with serine 309 in mice) induces ligand-independent ERα activity. Here, we studied the effect of ERα phosphorylation at S309 on the reproductive function of male mice. ERα309 (p.S309A, ERαS309A) knock-in (KI) mice were generated by homologous recombination in mouse embryonic stem (ES) cells. The ERαS309A KI males were subfertile with decreased sperm motility, dilated lumen and thinned epithelium of efferent ducts. Ultrastructural observation showed that the area of endocytic vesicles and lysosomes in the non-ciliated cells, and the number of cilia in the cilia cells were significantly reduced in the efferent ducts of ERαS309A mice. The pH value of epididymal fluid was significantly higher in all regions of epididymis in the ERαS309A KI mice. Moreover, the expression of aquaporin 9 (AQP9) in the efferent ducts and carbonic anhydrase XII (CAR12) in the epididymis was decreased in ERαS309A KI mice. The results indicate that ERα phosphorylated at Ser309 participates in maintaining the unique luminal milieu by regulating the expression of critical regulators of fluid/ion transport in efferent ducts and epididymis.