The sustainable and green chemistry concept calls for effective separation and recycling of valuable functional nanoparticles. In this work, a viable approach to separate and recover synthetic nanoparticles without involving heavy-duty instruments was established. The nanoparticle separation was enabled by using reversible boronate ester and boroxine bonds formed between boronic acid-functionalized nanoparticles and poly(vinyl alcohol) and between the nanoparticles themselves. The reversible covalent bonds were controlled by simple adjustment of solvent pH. To demonstrate the viability of the approach, two types of nanoparticles-inorganic silica nanoparticles and organic molecularly imprinted nanoparticles functionalized with boronic acid on their surface-were used as models. Upon addition of poly(vinyl alcohol) and adjustment to basic pH, the nanoparticles formed aggregates and readily settled from solution. After changing to an acidic solvent, the boronate ester bonds formed between boronic acid-functionalized nanoparticles and poly(vinyl alcohol) were hydrolyzed, and poly(vinyl alcohol) was released from the nanoparticle aggregates. The particles remained as aggregates due to the formation of new, interparticle boroxine bonds. By use of pH-controlled dynamic particle aggregation, propranolol-imprinted nanoparticles could be easily recovered and used repetitively without centrifugation. This work provides a new approach for recovery of valuable functional nanomaterials for potentially large-scale industrial applications.