Sulfamethoxazole (SMX) and sulfapyridine (SPY), two representative sulfonamide antibiotics, have gained increasing attention because of the ecological risks these substances pose to plants, animals, and humans. This work systematically investigated the removal of SMX and SPY by carbon nanotubes (CNTs) in fixed-bed columns under a broad range of conditions including: CNT incorporation method, solution pH, bed depth, adsorbent dosage, adsorbate initial concentration, and flow rate. Fixed-bed experiments showed that pH is a key factor that affects the adsorption capacity of antibiotics to CNTs. The Bed Depth Service Time model describes well the relationship between service time and bed depth and can be used to design appropriate column parameters. During fixed-bed regeneration, small amounts of SMX (3%) and SPY (9%) were irreversibly bonded to the CNT/sand porous media, thus reducing the column capacity for subsequent reuse from 67.9 to 50.4 mg g−1 for SMX and from 91.9 to 72.9 mg g−1 for SPY. The reduced column capacity resulted from the decrease in available adsorption sites and resulting repulsion (i.e., blocking) of incoming antibiotics from those previously adsorbed. Findings from this study demonstrate that fixed-bed columns packed with CNTs can be efficiently used and regenerated to remove antibiotics from water.