In coagulation-membrane filtration water treatment processes, it is still difficult to determine the optimal coagulation condition to minimize irreversible membrane fouling. In microfiltration (MF), meso-particles (i.e., 20 nm-0.5 μm) are thought to play an important role in irreversible membrane fouling, especially their characteristics of particle number (PN) and zeta potential (ZP). In this study, a new nanoparticle tracker combined a high-output violet laser with a microscope was developed to identify the physicochemical characteristics of these microscopic and widely dispersed meso-particles. The effects of pH and coagulant dose on ZP and PN of micro-particles (i.e., >0.5 μm) and meso-particles were investigated, and then coagulation-MF tests were conducted. As the result, irreversible membrane fouling was best controlled for both types of membranes, while meso-particle ZP approached zero at around pH 5.5 for both types of natural water. Since PN was greatest under these conditions, ZP is more important in determining the extent of irreversible membrane fouling than PN. However, the acidic condition to neutralize meso-particles is not suitable for actual operation, as considering residual aluminum concentration, pipe corrosion, and chlorination efficiency. It is therefore necessary to investigate coagulants or other methods for the appropriate modification of meso-particle characteristics.