Consolidation deformation can lead to changes of structural and permeable characteristics of clay impermeable layer, which will affect the distribution of seepage field and concentration field, and then affect the transport law of contaminant in impermeable layer. Based on the Biot consolidation theory, the transport law of contaminant in deforming soil is studied taking account. Meanwhile, the effects of consolidation pressures and adsorption parameters have been analyzed separately. The results show that consolidation deformation retards the transport process of contaminant and shortens the transport depth of contaminant. In addition, the retardation of consolidation deformation on the transport process of contaminant becomes stronger as the consolidation pressure increases. Meanwhile, under the condition of a linear adsorption mode, the decreasing rate of migration depth increases gradually as the adsorption parameter decreases. It is shown that the retardation of consolidation deformation on the transport process of contaminant becomes more visible when the adsorption parameter decreases. The results have important theoretical significance for the design of effective thickness of the simple constructed garbage dump and bottom sediment dump, as well as the safety evaluation of impermeable layer.