In this study, we evaluated the effect of dissolved organic matter on the sorption of ciprofloxacin by magnetite silica-based nanoparticles (NPs). For this purpose, magnetite nanoparticles modified with organosilanes (tetraethox-ysilane and 3-aminopropyltriethoxysilane, MTA) were used as a model of colloidal particles and a sorbent. Analysis of the absorption spectra found that there was no interaction between antibiotic ciprofloxacin (CIP) and humic substances (HS, sodium salt of humic acids) in aquatic system at pH varied from 6 to 8. But, the behavior of CIP and HS changes dramatically upon addition of silica-coated magnetite nanoparticles. The introduction of the MTA NPs into a bicomponent system of CIP incubated with HS lead to more than twice increased CIP sorption. Results of electrokinetic measurements in terms of zeta-potentials propose the interaction mechanism into CIP-HS-NPs system. In the three-component system, the surface of MTA is completely overcharged from negative to positive, and importantly this effect is pH-dependent. The MTA zeta-potential changes from − 15 (pH 6) and − 30 mV (pH 8) to + 10 (pH 6) and + 2 (pH 8), respectively. The study provides novel scientific information as nanoparticles are increasingly produced and studied for various environmental applications, including sorption of new emerging eco-toxicants (pharmaceuticals) but the assessment of dissolved organic matter contained even in trace concentrations should not be ignored.