Bisphenol A (BPA) is a widely used chemical in several consumer products and a well-studied environmental toxicant, and therefore, its accurate measurement is highly demanded. However, the co-presence of nanoparticles as an emerging class of contaminants could result in inaccurate determination of BPA due to binding of BPA onto nanoparticle surface. In this study, mass spectrometry (MS) was used to investigate desorption of BPA bound on the surface of titania (TiO2) nanoparticles in water. Ammonium acetate, fluoride, formate, and hydroxide were evaluated as chemical agents for their desorption capabilities. The percentages of recovery, adsorption, and desorption were determined by this new method without requiring any prior separation of nanoparticles from BPA. MS analysis demonstrated the desorption of BPA by 10–20 mM of ammonium hydroxide for a mixture of 5 µg/mL BPA and 10 µg/mL TiO2 nanoparticles, with a desorption efficiency of 72 ± 1%. Due to adsorption of BPA onto the nanoparticle surface that was inefficient for electrospray ionization, the resulting abundance of target ions could be reduced in the detection of BPA by mass spectrometry. As such, these findings collectively promise an accurate determination of the total BPA concentration in water whether it exists in the free or bound form. Efficient desorption of contaminants from the surface of nanoparticles would improve the accuracy of the contaminant analysis by mass spectrometry.