This work investigates the influence of cation type (Ca2+ as compared to K+) on the co-transport and deposition of functionalized multi-walled carbon nanotubes (MWCNTs) with negatively (bentonite nanoparticles, BNPs) or positively (goethite nanoparticles, GNPs) charged natural nanoparticles under the same ionic strength (IS = 1 mM) conditions. In packed column tests with quartz sand (QS), the co-transport of MWCNTs was slightly increased by BNPs and inhibited by GNPs in both CaCl2 and KCl solutions, whereas the co-transport of BNPs or GNPs was facilitated by MWCNTs in both solutions. However, the co-transport of MWCNTs in the presence of BNPs or GNPs exhibited a different dependency on the cation type in quartz crystal microbalance with dissipation (QCM-D) tests. No deposition of MWCNTs and BNPs was observed in QCM-D studies in the presence of KCl, while enhanced deposition of MWCNTs and GNPs occurred in this same solution. In contrast, the deposition of both MWCNTs and BNPs or MWCNTs and GNPs increased in QCM-D in the presence of CaCl2. In both column and QCM-D studies, Ca2+ exhibited a more significant impact on co-transport than K+, especially for MWCNTs with GNPs than BNPs. Results from molecular dynamic simulations, aggregation studies, and interaction energy calculations indicate that non-DLVO interactions (e.g., H-bonding and cation-π interaction) between two nanoparticles (MWCNTs with BNPs or GNPs) played a non-negligible role in interpreting the deposition and co-transport in the presence of the divalent cation Ca2+. Mathematical modeling of breakthrough curves and retention profiles and aggregation results suggest that both straining and competitive blocking were enhanced and played dominant roles in the co-transport of MWCNTs in the presence of BNPs or GNPs in QS, especially in the presence of Ca2+. This work sheds novel insights on the contribution of divalent cations to interactions between two colloids and their co-transport in porous media. This information is needed to assess the environmental fate and risks of engineered nanoparticles (ENPs) and natural nanoparticles in aquatic and soil environments with abundant divalent cations.