The movement of subaqueous sediment in laminar shearing flow is numerically investigated by the coupled lattice Boltzmann and discrete element methods. First, the numerical method is validated by comparing the phase diagram proposed by Ouriemi {it et al.} ({it J. Fluid Mech}., vol. 636, 2009, pp. 321-336). Second, a detailed study on sediment movement is performed for sediment with varying solid volume fractions, and a nonlinear relationship between the normalised thickness of the mobile layer and the normalised fluid flow rate is observed for a densely-packed sediment. Third, an independent investigation on the effective viscosity and friction coefficient of the sediment under different fluid flow rates is conducted in a shear cell; and substitution of these two critical parameters into a theoretical expression proposed by Aussillous {it et al.} ({it J. Fluid Mech}., vol. 736, 2013, pp. 594-615) provides consistent predictions of bedload thickness with the simulation results of sediment movement. Therefore, we conclude that the non-Newtonian behaviour of densely-packed sediment leads to the nonlinear relationship between the normalised thickness of the mobile layer and the normalised fluid flow rate.