When a seal is applied to prevent leakage of a pressurized fluid it must be designed to sustain the hydrostatic load it is subjected to. One important aspect that the design must take into consideration is the possibility that the hydrostatic fluid load may deform the sealing surfaces to such an extent that leakage occurs. In this paper, we describe the development and implementation of a novel boundary element method (BEM) that can be used to study the effects of the pressurized fluid presents at the interface between the sealing surfaces. The proposed method utilizes a connected region labeling algorithm to identify the fluid-filled regions and it solves the coupled solid-solid and fluid-solid contact problem with an FFT-based boundary element method (DC-FFT). When benchmarked against a FEM implementation of the same problem, it is found that the results are in good agreement. In particular, it is shown that the proposed method can capture the deformation of the sealing surfaces, and how the fluid front advances when the hydrostatic pressure increases.