The foundation of nanoscience is that the properties of materials change as a function of their physical dimensions, and nanotechnology exploits this premise by applying selected property modifications for a specific benefit. However, to investigate the fate and effect of the engineered nanoparticles on toxic metal (TM) mobility, the analytical limitations in a natural environment remain a critical problem to overcome. Recently, a new generation of size exclusion chromatography (SEC) columns developed with spherical silica is available for pore sizes between 5 and 400 nm, allowing the analysis of nanoparticles. In this study, these columns were applied to the analysis of metal-based nanoparticles in environmental and artificial samples. The new method allows quantitative measurements of the interactions among nanoparticles, organic matter, and metals. Moreover, because of the new nanoscale SEC, our method allows the study of these interactions for different size ranges of nanoparticles and weights of organic molecules with a precision of 1.2 × 10(-2) kDa. The method was successfully applied to the study of nanomagnetite spiked in complex matrixes, such as sewage sludge, groundwater, tap water, and different artificial samples containing Leonardite humic acid and different toxic metals (i.e., As, Pb, Th). Finally, our results showed that different types of interactions, such as adsorption, stabilization, and/or destabilization of nanomagnetite could be observed using this new method.