<p>Natural nanoparticles (NPs) and natural organic matter (NOM) are ubiquitous in the environments such as soils, sediments, and surface waters. The adsorption of NOM onto mineral NPs is a key natural process, which has significant effects on the fate and biogeochemical cycles of many chemicals including toxic ones. For the first time, complex of complimentary analytical methods including capillary zone electrophoresis (CZE), dynamic light scattering, and laser Doppler velocimetry (LDV) has been used for study of effect of NOM on the fate of natural NPs in simulated surface waters. Muscovite NPs and fulvic acid (FA) have been taken as examples. It has been demonstrated that CZE can be an efficient tool for the study on interactions of mineral NPs and FA. CZE allowed one to discriminate muscovite NPs, FA, and products of their interaction—organometallic complex. It is most likely that FA forms a complex with Al. It is found that Al³⁺-FA complex has an intermediate electrophoretic mobility (46.6 cm²V⁻¹&#xa0;s⁻¹) between muscovite NPs (31.6 cm²V⁻¹&#xa0;s⁻¹) and FA (49.3 cm²V⁻¹&#xa0;s⁻¹) as measured for suspension with pH value of 6. It is also demonstrated that electrophoretic mobility of Al³⁺-FA complex is less susceptible to pH of medium as compared to muscovite NPs. The absolute value of electrophoretic mobility increases with increasing pH of buffer solution from 31.0 to 37.9·10⁻⁵ cm²V⁻¹&#xa0;s⁻¹ for muscovite NPs and from 46.3 to 50.0·10⁻⁵ cm²V⁻¹&#xa0;s⁻¹ for Al³⁺-FA complex. The obtained zeta-potential values (from − 45 to − 55&#xa0;mV) have demonstrated that muscovite NPs are characterized by good stability in simulated surface waters. Thus, the results obtained have confirmed that NOM can significantly affect the fate of natural NPs in aquatic environments.</p>