Nowadays non-steroidal anti-inflammatory drugs (NSAIDs) are often detected in surface water and groundwater. In this study, effects of environmental factors, i.e., solution pH, ionic strength, temperature and surface-bound organic acids, on bonding of three typical NSAIDs (ketoprofen, naproxen and diclofenac) onto goethite were systematically investigated. Column chromatography, batch experiments, attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy and surface complexation modeling were used to probe the adsorption mechanisms. Bonding of three NSAIDs onto goethite was totally reversible, ionic strength-dependent and endothermic (adsorption enthalpy 2.86–9.75 kJ/mol). These evidences supported H-bonding mechanism, which was further explained by ATR-FTIR observation and a triple planes model. Surface-bound organic acids (phthalic acid, trimellitic acid and pyromellitic acid) by inner-sphere complexation with goethite were hard to be desorbed. Surface-bound phthalic acid increased the uptake of NSAIDs but surface-bound trimellitic acid and pyromellitic acid reduced their adsorption. The reason is that the adsorbed phthalic acid can result in a more hydrophobic surface while adsorbed trimellitic acid and pyromellitic acid increased the surface negative charge and polarity. Finally, adsorption of NSAIDs onto goethite with/without surface-bound organic acids was well described by a free energy model, in which contributions of interactions (e.g., H-bonding and van der Waals) were evaluated.