Ultrafiltration membranes have a great potential to retain different types of algae with high efficiency. Nevertheless, the membrane fouling propensity, the cleanability, and consequently, the membrane lifespan are revealed to be significantly influenced by the algae type, cell condition and the operating parameters. Therefore, the fouling mechanisms of commercial ultrafiltration (UF) capillary membranes during dead-end filtration of various fresh water and marine algae types, in different cell condition, i.e., “intact” or “lysed”, are analyzed. Moreover, the potential of chemical enhanced backwashing approach and the permeability recovery are investigated. According to the results, the membranes showed different fouling behavior depending on the algae cell condition, which was also interestingly limited to the algae type. Furthermore, the fouled membranes by marine algae types exhibited better cleanability than those fouled by fresh water algae types. The differences in the fouling mechanisms and the cleanability were successfully correlated to the algae’s characteristics that were found to differ, for the same algae type, according to the cell condition.