Forward osmosis (FO) is attracting increasing interest for its potential applications in desalination. In FO, permeation of contaminants from feed solution into draw solution through the semipermeable membrane can take place simultaneously with water diffusion. Understanding the contaminants transport through and rejection by FO membrane has significant technical implications in the way to separate clean water from the diluted draw solution. In this study, a model was developed to predict boron flux in FO operation. A strong agreement between modeling results and experimental data indicates that the model developed in this study can accurately predict the boron transport through FO membranes. Furthermore, the model can guide the fabrication of improved FO membranes with decreased boron permeability and structural parameter to minimize boron flux. Both theoretical model and experimental results demonstrated that when membrane active layer was facing draw solution, boron flux was substantially greater compared to the other membrane orientation due to more severe internal concentration polarization. In this investigation, for the first time, rejection of contaminants was defined in FO processes. This is critical to compare the membrane performance between different membranes and experimental conditions.