This study compared the performances of two laboratory-scale sequencing batch reactors to remove 17β-estradiol and 17α-ethinyl estradiol. Both SBRs were operated to achieve organic carbon oxidation and nitrification. However, the overall bacterial population in both SBRs was targeted to be different by feeding the SBRs with peptone and glucose. Furthermore, the reactors were also run at different solid retention times (SRTs) to evaluate the effect of SRT on estrogen removal. The more diverse heterotrophic and ammonia oxidizing bacterial community in the peptone fed SBR1 had superior estrogen removal than the glucose fed SBR 2 which enriched less diverse community, particularly for 17α-ethinyl estradiol. Under a solids retention time (SRT) of 40days, the total 17β-estradiol mass was 30% of the amount under the SRT of 20days, and the total 17α-ethinyl estradiol mass was likewise 40% of the amount under the shorter SRT.