Concerns over the environmental impacts and risks assessment of carbon nanotubes (CNTs) have been raised along with their prevailing applications. It is therefore critical to understand the transport, behavior, and fate of CNTs in the environment. Previous studies of CNT transport were mainly focused on ideal porous media (i.e., acid-washed sands or glass beads). In the natural environment, however, surfaces of natural porous media may be coated with impurities, such as metal oxide and organic matters. In this work, natural quartz sand was used to investigate transport behavior of multi-walled carbon nanotubes (MWNTs) and single-walled carbon nanotubes (SWNTs) in saturated porous media. Our results showed that the mass recoveries of MWNTs and SWNTs were only 9% and 2% in natural sand media, compared with 96% (MWNTs) and 95% (SWNTs) in the clean sand. We also found most of the “trapped” MWNTs and SWNTs in the natural sands could not be remobilized by inverse, high-velocity, or surfactant flushing. Further investigations of metal element compositions on the natural sand surfaces revealed trace level of iron (Fe) and aluminum (Al) at 465.2 and 945.6 mg/kg, respectively. The low mobility of CNTs in the natural sand media thus could be attributed to the strong interactions between carboxyl groups and metal oxides/hydroxides.