Reverse osmosis is the leading technology for seawater desalination. We have recently introduced a systematic two-step approach based on process network optimization techniques . The methodology allows for a reliable and relatively quick determination of optimal process structures for seawater reverse osmosis (SWRO) desalination systems, as well as for the analysis of trends across different design classes  for a given economic objective and typical design constraints. The approach was subsequently extended to address detailed water quality information as part of the process network synthesis, by developing simple but realistic membrane element models based on commercial simulators, in order to account for the rejection of individual seawater constituents throughout the temperature ranges of interest . This enables the design for common product water specifications whilst capturing membrane-scaling issues. This work expands our previous efforts, and more specifically addresses the issue of boron removal, which is often a key challenge in SWRO design. RO membrane element models that allow for the tracing of individual constituents throughout the processing system, including boron, were developed and incorporated into the process network optimization problem formulation. The superstructure optimization formulations were also expanded so as to handle additional design decisions associated with Boron removal in SWRO process networks. This includes selecting suitable combinations for several options of membrane elements types listed by the ROSA membrane simulator (Dow), determining optimum pH conditions required for these membrane element choices, and acid/base dosing adjustments required. The approach has been illustrated with a case study that involves seawater qualities with salinities ranging from 35 to 50 ppt. The results highlight the variation in optimal designs depending on the given feed water quality, the desired salinity removal and the acceptable boron level in the permeate stream.