It is well known that reverse osmosis (RO) is the leading desalination technology. As an energy intensive technology, the exploitation of renewable energy sources (RES) to power RO systems is a attractive option. A strategy to take advantage of all the available energy of an off-grid renewable system is to work with the RO system under variable operating conditions. This implies additional challenges in terms of water production and permeate quality, among others. Boron rejection is one of the main concerns in seawater RO (SWRO) systems. The aim of this work was to evaluate the performance and boron rejection of a single-stage SWRO system with 7 membrane elements per pressure vessel under variable operating conditions. The initial permeability coefficients of two SWRO membranes (TM820L-440 and TM820S-400) were calculated from experimental data of a full-scale SWRO desalination plant. These coefficients and the characteristics of the membranes were introduced in a simulation algorithm to estimate the behavior of the SWRO system. The results show that, compared with the TM820S-400 membrane, the TM820L-440 performed better in terms of boron rejection in the form of boric acid, but worse in terms of water production. When RES-powered SWRO systems are designed to work under variable operating conditions, consideration needs to be given to the safe operation window in terms of boron concentration in the permeate and to variation of the permeability coefficient of the membranes.