- The consequences of chemical cleaning of ultrafiltration membranes should not be interpreted solely in terms of flux recovery. It is important to evaluate the nature of the interactions between the cleaning agent and the membrane surface and to determine whether the introduction of the agent acts solely to improve the flux recovery or whether it also alters the membrane skin layer. Despite the important consequences of this information, only very limited data have been reported to date about the permeability-treatment relationships. Studies on membranes have mainly considered changes in streaming potential, FTIR spectra and hydrophobicity of the membrane surface. The present report uses an additional tool, probes of gold nanoparticles or dye-labeled MS2 bacteriophages, to trace gradual disintegration of the membrane skin layer during chemical cleaning. The new type of probe allowed us to follow two-stage deformation kinetics of the membranes during oxidative cleaning. The first stage involved the formation of holes with an average diameter of 20–30 nm, and the second stage, the rapid growth of the holes, leading to disintegration of the skin layer. The two-phase transition was followed using bubble-point measurements, ATR-FTIR spectroscopy, and SEM micrography. A second aim of the current article is to demonstrate the usefulness of a newly introduced tool—monodispersed nanoprobes—to trace membrane damage.