•The same CCC was gained at M(CTAB)=0.1mmolL−1 for different 30R50 concentrations.•More than 95.7% of turbidity can be removed for 30R50 0.15% with CTAB 0.1mmolL−1.•The “hydrophobic effect” plays an important role in aggregation of 30R25.•The results show different agglomeration mechanisms. Nanoparticles will inevitably be found in industrial and domestic wastes in the near future and as a consequence soon in water resources. Due to their ultra-small size, nanoparticles may not only have new hazards for environment and human health, but also cause low separation efficiency by classical water treatments processes. Thus, it would be an important challenge to develop a specific treatment with suitable additives for recovery of nanoparticles from waters. For this propose, this paper presents aggregation of silica nanoparticles (Klebosol 30R50 (75nm) and 30R25 (30nm)) by cationic surfactant cetyltrimethylammonium bromide (CTAB). Different mechanisms such as charge neutralization, “depletion flocculation” or “volume-restriction”, and “hydrophobic effect” between hydrocarbon tails of CTAB have been proposed to explicate aggregation results. One important finding is that for different volume concentrations between 0.05% and 0.51% of 30R50 suspensions, the same critical coagulation concentration was observed at CTAB=0.1mM, suggesting the optimized quantity of CTAB during the separation process for nanoparticles of about 75nm. Furthermore, very small quantities of CTAB (0.01mM) can make 30R25 nanosilica aggregated due to the “hydrophobic effect”. It is then possible to minimize the sludge and allow the separation process as “greener” as possible by studying this case. It has also shown that aggregation mechanisms can be different for very small particles so that a special attention has to be paid to the treatment of nanoparticles contained in water and wastewaters.