This work investigated the effect of different surface modification methods, including oxidization, surfactant coating, and humic acid coating, on single-walled carbon nanotube (SWNT) stability and their mobility in granular porous media under various conditions. Characterization and stability studies demonstrated that the three surface modification methods were all effective in solubilizing and stabilizing the SWNTs in aqueous solutions. Packed sand column experiments showed that although the three surface medication methods showed different effect on the retention and transport of SWNTs in the columns, all the modified SWNTs were highly mobile. Compared with the other two surface modification methods, the humic acid coating method introduced the highest mobility to the SWNTs. While reductions in moisture content in the porous media could promote the retention of the surface modified SWNTs in some sand columns, results from bubble column experiment suggested that only oxidized SWNTs were retention in unsaturated porous media through attachment on air–water interfaces. Other mechanisms such as grain surface attachment and thin-water film straining could also be responsible for the retention of the SWNTs in unsaturated porous media. An advection–dispersion model was successfully applied to simulate the experimental data of surface modified SWNT retention and transport in porous media.