Contaminant transport has been widely studied in rigid porous media, but there are some cases where a large volumetric stain occurs such as dewatering of dredged contaminated sediment, landfill liner, and in-situ capping. This paper presents a numerical investigation of contaminant transport coupled with large strain consolidation. Consolidation test was performed with contaminated sediments collected in Gary, Indiana, U.S. to obtain constitutive relationships, which are required for numerical simulations. Numerical results using CST2 show an excellent agreement with measured settlement and excess pore pressure. CST2 is then used to simulate contaminant transport during and after in-situ capping. Numerical simulations provide that transient advective flows caused by consolidation significantly increase the contaminant transport rate. In addition, the numerical simulations revealed that active capping with Reactive Core Mat (RCM) significantly decelerates consolidation-induced contaminant transport.