Harmful pathogens and compounds must be removed from wastewater before it can be discharged to the environment or used for irrigation, and many source waters need salts removed to make them potable. Microfiltration and ultrafiltration membranes remove pathogens and unwanted chemicals but as they are used, they become fouled and blocked by particulates and compounds from the water being filtered, as well as by the formation of biofilm, and by chemical interactions between solutes and the membrane materials. Although the membranes are cleaned regularly, the cleaning chemicals themselves can cause a problem. This research characterised the damage that various cleaning regimens inflict on membranes made of different materials and examined the effects of progressive and consecutive stages of membrane aging and degradation on performance. It was concluded that the type of cleaning agent affects the mechanism of membrane degradation and the severity of membrane integrity loss. More information is needed regarding the cleaning protocols and agents used in industry. Information from this research can inform a generally applicable model to predict membrane aging and decline in performance.