Recent studies have shown the presence of endocrine disrupting compounds (EDCs) in seawater and brackish water, which could potentially complicate various seawater desalination treatment processes. In this study, the adsorption of bisphenol A (BPA) and 17α-ethinyl estradiol (EE2) by single walled carbon nanotubes (SWCNTs) was investigated. Solutions of artificial seawater, brackish water, and a combination of these two waters were prepared, in accordance with previously published composition data. Overall, the removal efficiency for EE2 (95–98%) was higher than BPA (75–80%), possibly because of its higher log KOW value. The adsorptive capacity of the SWCNTs remained relatively constant for the artificial source waters used in this study, suggesting that the changes in the composition of the water did not affect the overall adsorption of the EDCs. Adjusting the pH of the solutions from 3.5 to 11 showed a 22–26% decrease in the adsorption of BPA, whereas no notable changes were found in the adsorption of EE2. Changes in the ionic strength of the solutions by increasing the concentrations of Na+ and Ca2+ did not significantly affect the adsorption of BPA or EE2. The concentration of dissolved organic carbon (DOC), represented in this study by humic acid, had noticeable effects on the adsorption of BPA and EE2. As the concentration of DOC increased, the removal of BPA and EE2 decreased by 5–15%, which could possibly be explained by competitive adsorption between the EDCs and humic acid. With increasing concentrations of SWCNTs, adsorption of DOC occurred with removal efficiencies of up to 95%. Hydrophobic interactions and π–π electron donor–acceptor (EDA) interactions among the EDCs, the DOC, and the SWCNTs have been hypothesized as the potential adsorption mechanisms for BPA and EE2.