Nanoparticle (NP) colloidal stability plays a crucial role in biomedical application not only for human and environmental safety but also for NP efficiency and functionality. NP agglomeration is considered as a possible process in monodispersed NP colloidal solutions, which drastically affects colloidal stability. This process is triggered by changes in the physicochemical properties of the surrounding media, such as ionic strength (IS), pH value, or presence of biomolecules. Despite different available characterization methods for nanoparticles (NPs), there is a lack of information about the underlying mechanisms at the early stage of dynamic behaviors, namely changing in NP size distribution and structure while placing them from a stable colloidal solution to a new media like biological fluids. In this study, an advancedin situapproach is presented that combines small angle X-ray scattering (SAXS) and microfluidics, allowing label-free, direct, time-resolved, and dynamic observations of the early stage of NP interaction/agglomeration initiated by environmental changes. It is shown for silica NPs that the presence of protein in the media enormously accelerates the NP agglomeration process compared to respective changes in IS and pH. High IS results in a staring agglomeration process after 40 min, though, in case of protein presence in media, this time decreased enormously to 48 s. These time scales show that this method is sensitive and precise in depicting the dynamics of fast and slow NP interactions in colloidal conditions and therefore supports understanding the colloidal stability of NPs in various media concluding in safe and efficient NP designing for various applications.