Derjaguin−Landau−Verwey−Overbeek (DLVO) theory is typically used to quantify surface interactions between engineered nanoparticles (ENPs), soil nanoparticles (SNPs), and/or porous media, which are used to assess environmental risk and fate of ENPs. This study investigates the co-transport behavior of functionalized multiwalled carbon nanotubes (MWCNTs) with positively (goethite nanoparticles, GNPs) and negatively (bentonite nanoparticles, BNPs) charged SNPs in quartz sand (QS). The presence of BNPs increased the transport of MWCNTs, but GNPs inhibited the transport of MWCNTs. In addition, we, for the first time, observed that the transport of negatively (BNPs) and positively (GNPs) charged SNPs was facilitated by the presence of MWCNTs. Traditional mechanisms associated with competitive blocking, heteroaggregation, and classic DLVO calculations cannot explain such phenomena. Direct examination using batch experiments and Fourier transform infrared (FTIR) spectroscopy, asymmetric flow field flow fractionation (AF4) coupled to UV and inductively coupled plasma mass spectrometry (AF4-UV-ICP-MS), and molecular dynamics (MD) simulations demonstrated that MWCNTs-BNPs or MWCNT-GNPs complexes or aggregates can be formed during co-transport. Non-DLVO interactions (e.g., H-bonding and Lewis acid−base interaction) helped to explain observed MWCNT deposition, associations between MWCNTs and both SNPs (positively or negatively), and co-transport. This research sheds novel insight into the transport of MWCNTs and SNPs in porous media and suggests that (i) mutual effects between colloids (e.g., heteroaggregation, co-transport, and competitive blocking) need to be considered in natural soil; and (ii) non-DLVO interactions should be comprehensively considered when evaluating the environmental risk and fate of ENPs.