Both the effect of natural estrogens (estone, estradiol and estriol), and the ability to improve estrogen removal using bioaugmentation with three estrogen-metabolizing bacteria, was examined in slow sand filters (SSFs). Concentrations of the natural estrogens determined by gas chromatography coupled with mass spectrometry (GC-MS) revealed that augmented filters removed significantly more estone and estradiol than non-augmented filters. Additionally, a positive correlation was found between coliform retention and estrogen concentration in non-augmented filters. This was explained by the toxic inhibition of protozoa, suggesting the functional implications (impaired coliform removal) that high estrogen concentrations might have in SSFs. Consequently, we suggest that high estrogen concentrations could impact significantly on water quality production, and in particular on pathogen removal. Monitoring and adapting the microbial community in SSFs will become an important element of water production and quality assurance in the future.