A decision support model for the selection of treatment preferences for permeate polishing is presented. The model is based on the analytical hierarchical process that integrates multi-criteria issues into the selection of post-treatment technology for a specific seawater reverse osmosis (SWRO) plant. The objectives in using this decision-supporting tool are several, including the poor experience of the decision-maker with respect to the technology to be purchased, the high number of both qualitative and quantitative attributes that have to be considered in the selection process, and, the number and variety of the alternative technologies available on the market. This paper introduces methodologies that rank the design options, provide recommendations based on permeate quality and process design, and improve the quality of information for the selection of boron removal treatment. The tool provides appropriate design guidelines for the impact of post-treatment on design and operation of SWRO plants prior to pilot and economic studies. The advantages of this approach are discussed in general terms while a specific example is presented for the Mediterranean Sea basin (Israel).