Reducing dredging activities in the harbors brings benefits both economically and environmentally. However, this means that ships may have to sail very close to or even through the mud layer on the seabed, with possible effects on ships’ resistance and manoeuvrability. This study has made a step in understanding these effects on ships’ resistance. In order to study the effects of the different mud characteristics on the passing vessels, non-Newtonian models have been implemented in ReFRESCO, the CFD code developed by the Maritime Research Institute Netherlands (MARIN) in collaboration with several non-profit organizations around the world. The objective of this study was to test the ability of ReFRESCO to simulate and assess the influence of a fluid mud layer on the resistance of a ship. RANS simulations are performed for the flow around a KVLCC2 benchmark vessel at model scale with h/T=1.2 and a Froude number of Fn=0.064. Calculations were carried out varying systematically the mud layer thickness (h_mud/T=0.1-0.3), the mud density ratio (ρ_mud/ρ_water=1.05-1.2) and the mud yield stress (τ_y=0-1 Pa). The mud is modelled with the regularized Bingham model. The results show that the resistance of the ship increases in the presence of a mud layer, mainly in the pressure component. The pressure resistance shows a significant peak when the internal Froude number 〖Fn〗_i approaches one. This suggests that the increase in resistance is mainly due to the dead-water resistance, which is highly dependent on the (combination of) ship’s velocity, mud layer thickness and density. The influence on the resistance due to the yield stress appears rather limited, and it depends on the density ratio between water and mud. Results also suggest that yield stress has mainly an effect on the viscous pressure component.