This study employs a two-dimensional numerical model, coupling Biot’s poro-elastic theory with advection-dispersion equations, to examine the impact of wave nonlinearity on solute transport in deformable seabed sediment. The simulations reveal that compared to the second-order Stokes waves, the first-order cnoidal waves exhibit significant nonlinear effects, effectively enhancing the longitudinal dispersion coefficient and solute transport rate in marine sediment. However, this enhancement diminishes as wave height increases and water depth decreases, highlighting the diminishing impact of cnoidal wave nonlinearity under such conditions.