The use of nanoparticles has gained great relevance in recent years, proposing novel solutions in the areas of analysis, diagnosis, and treatment of diseases. Likewise, their versatility and specificity would allow the development of rapid detection systems for different chemical compounds or even microorganisms present in aqueous suspensions. This work presents a microfluidic system that facilitates the manipulation and control of nanoagglomeration reactions. Initially, it starts with a stable suspension of gold nanoparticles (AuNps) of 13 nm in diameter, which is exposed to a solution with greater ionic strength (NaCl), which destabilizes the particles and triggers a process of agglomeration or growth in particle size. Microscopic image recordings allow real-time monitoring of the dynamics within the channel. This temporal evolution is characterized through image processing, which has allowed us to detect particles 2 min after the onset of agglomeration reactions, and to evaluate their concentration and size as a function of time. These results will allow us to develop a nanoparticulate system functionalized with specific aptamers for Escherichia coli in the future, as well as to develop a biosensor using nanoagglomeration processes to identify the presence of bacteria in aqueous suspensions.