Owing to the increased application of nanoparticles in engineering industries, the development of separation techniques to isolate nanoparticles grew as important as the one to isolate micro- or macro-sized particles. Centrifugation, filtration, and precipitation are the common processes used to separate nanoparticles from a suspension. Interestingly, these processes work best if the nanoparticles are preflocculated into a larger cluster. Flocculation of nanoparticles may involve a complex mechanism affected by the physicochemical and molecular properties of the flocculant. A review of the effects induced by these factors on the flocculation of nanoparticles is given. The applications of advanced flocculation approaches as well as the research gaps in this research area are discussed.