We study numerically the effects of a viscous fluid seabed on wave scattering with a solid obstacle of rectangular shape fixed at the free surface, on the seafloor, or internally within the water layer. The computational model is based on OpenFOAM and it is validated using existing analytical solutions for waves encountering an obstacle on a solid bed and available experimental data for waves propagating over a muddy seabed with no obstacles. With the consideration of a solid obstacle on a viscous fluid bottom, we examine the corresponding transformations of incident, reflected, and transmitted wave components. The velocity field near the obstacle and the wave forces exerted on the obstacle are also analyzed. Our simulations show that all wave components experience significant amplitude attenuation caused by the viscous fluid bed. For both surface and bottom obstacles, the presence of an obstacle enhances the damping of reflected waves. When an internally submerged obstacle is considered, transmitted waves are the most affected due to a prominent vortex generated in the lee of the obstacle. Patterns of the velocity field in the vicinity of the obstacle are shown to be controlled mainly by the obstacle with some modulations in magnitude and wavelength contributed by the viscous fluid bed. In view of the vertical wave force on the obstacle surface, both a phase shift and decrease in magnitude are observed. These findings enhance our understanding of the underlying physical processes in the wave–obstacle–mud problems. More studies are still needed in order to provide the necessary technical tools for the engineering design of coastal structures in muddy marine environments.