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The paper presents a new methodology for short-term (5–25 min) benchtop tests to evaluate the effectiveness of magnetic treatment of feed water for reducing mineral scaling on a reverse osmosis (RO) membrane. Scale deposition is measured at a controlled level of salt supersaturation in water flowing through an RO unit in once-through mode. A magnetic water conditioner is tested in a transient flow regime when variations of the permeate flux along the flow path are insignificant. Scale formation under these conditions is governed by salt crystallization on the membrane surface. The proposed method was implemented to investigate the influence of magnetic treatment on gypsum deposition on RO membranes in supersaturated aqueous CaSO4/NaCl solutions. The effects of magnetic water treatment on scale formation under our experimental conditions were found to be statistically insignificant with a confidence level of 95%. However, this outcome should not be considered to negate the potential efficiency of magnetic water treatment in specific applications. The proposed methodology of testing under a controlled level of salt supersaturation will also be useful for evaluating the efficiency of other water treatment technologies.