In a water treatment system, a pretreatment chemical (14) is added to water stream (5C) in a pretreatment process (1) including a coagulation, flocculation (10) and separation (18, 19) to reduce amount of dissolved and/or particulate matter in the water stream. Hydrophobic conditions in the water stream are monitored (12) upstream (15C) or downstream (1**, 15B) from adding the pretreatment chemicals. Dosing (11) of the pretreatment chemical (14) to the water stream is controlled (13) based on the monitored hydrophobic conditions. Thereby a membrane fouling in subsequent membrane filtration stage (3) can be minimized.