Common squat prediction formulae to assess the navigation safety usually do not take into account the bottom condition. Nevertheless, the presence of a fluid mud layer is not an uncommon condition in confined areas where accurate squat predictions are necessary. From 2001 to 2004 an extensive experimental research program was carried out to measure the manoeuvring behaviour of deep drafted vessels in muddy areas. A part of the program focused on the undulations of the water–mud interface and their relationship to the ship’s squat. Mostly the sinkage of the ship is damped due to the presence of the mud layer, but a larger trim can occur due to the water–mud interface undulations. This article presents a mathematical model to predict the squat in muddy navigation areas.