Abstract: Covering water is one of the factors that make the underwater vacuum preloading different from the onshore one. It affects the behaviors of consolidation and settlement of the foundation to some degree. FEM analysis is adopted to investigate the loading and the boundary seepage effects of the covering water on the foundation settlement. An analysis method is proposed with the theories of consolidation and seepage to consider the combined effect of the covering water on the settlement on the basis of the FEM results, which is proved to be reasonable and valid with a case study. Comparison is also made between the conventional and the proposed methods. The research results show that the prediction by the proposed method is better in fitting with the measured data than the conventional one, suggesting the reasonability and validity of the proposed method in considering the effect of the covering water. Advices are also given to the application of the method in engineering practice.