The study aimed at further developing an integrated capacitive deionisation (CDI)-based process to treat reverse osmosis (RO) brine from a water reclamation facility to increase the overall water recovery to more than 90% and to achieve a sustainable operation of the process with optimised conditions. The normalised treatment capacity of CDI membranes and voltage was optimised at 24.8 L/m2/h and 1.1–1.5 V, respectively. The operation time of CDI cell with membrane area of 0.8 m2 was able to be extended to more than 1,000 h from the initial 72 h. Cleaning with both HCl at low pH and salt solution was good in removing foulants but cleaning with citric acid was not effective, as expected. The initiative cleaning strategy was found to be more effective in CDI fouling control and is recommended for long-term CDI operation. CDI cell efficiency for removal of ions reduced with operation time due to cleaning with surfactants at pH 10.5 which should be avoided in a future study.