Seepage plays a crucial role in the installation of suction caisson foundations and this has been considered by several researchers via experimental, numerical and analytical studies. In most of the available numerical and analytical studies, the actual seabed profile has been modelled using a number of assumptions and considering a limited number of idealised conditions to simplify the problem. However, it is well established that the behaviour of seabed, and soil in general, is a complex and nonhomogeneous one and that these assumptions can affect the reliability of the results. This paper examines the installation of suction caisson foundation into a realistic and natural seabed profile. It identifies the changes in seepage flow at different stages of installation and the role of crucial parameters such as permeability on the installation process is discussed. The results show that a significant increase in resistance to penetration occurs at the interface layers.