Web sites are most effective when they meet both the contents and usability needs of their users. It is revealed, however, that designing usable Web sites is not a trivial task. A primary reason is that Web developers’ perceptions and knowledge can be very different from those of the target users. Such differences result in cases in which users cannot easily locate the relevant information in a Web site. In this paper, we propose a math programming model to improve the navigation effectiveness of a Web site while preserving its original structure whenever possible. Our approach minimizes unnecessary changes to the present structure of a Web site and hence can be applied for Web site maintenance on a regular basis. Our test on a real Web site shows that the approach can provide significant improvements over the Web site structure by introducing only a small number of new links.