The invention relates to a method and a system for treatment of an underwater surface (S) and material removed from it at a cleaning site. The underwater surface is cleaned by a brush device (1), by which effluent containing solid matter removed from the underwater surface in connection with cleaning is conveyed to a treatment unit (5) where the effluent is subjected to separation and filtering. In a first step, the solid matter contained in the effluent is separated from the effluent in a form as unbroken as possible, immediately followed by a second step in which the effluent is precipitated. Said second step is immediately followed by a third step in which the effluent is filtered. The filtered effluent is discharged directly back to a body of water or to another clean water connection at the cleaning site. The effluent may be subjected to additional filtering and/or disinfection, if necessary.