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For providing advanced desalination the combination of the improvement of water recovery ratio in the reverse osmosis (RO) process and the No-Chlorine/No-Sodium Bisulfite (SBS) Dosing process was studied. In order to prevent membrane fouling even in high recovery water operations, an advanced two-stage design was implemented to (1) control the permeate flux through the RO membrane module, (2) optimize the system to reduce contaminant build-up and (3) eliminate the use of chlorine and SBS, which can accelerate membrane fouling. The system was evaluated by monitoring the biofouling and the microorganisms proliferation on the membrane surface based on membrane biofilm formation rate (mBFR). The pilot plant was operated in the condition of a water recovery rate of 55%. As a result, the system was operated for longer than four months without membrane cleaning (clean in place; CIP) and the possibility of operation for seven months without CIP was confirmed by the extrapolation of the pressure values. In addition, the mBFR is a reliable tool for water quality assessment, based on a comparison between the fouling tendency estimated from the mBFR and the actual membrane surface condition from autopsy study and the effectiveness No-Chlorine/No-SBS Dosing process was verified from mBFR of pretreated seawater.