The production and degradation of plastic remains can result in nanoplastics (NPs) formation. However, insufficient information regarding the environmental behaviors of NPs impedes comprehensive assessment of their significant threats. In this study, the transport behavior of unmodified NPs (PSNPs), carboxyl-modified NPs (PSNPs−COOH), and amino-modified NPs (PSNPs−NH2) was investigated using column experiments in the presence and absence of goethite (GT) and diethylhexyl phthalate (DEHP). Quantum chemical computation was performed to reveal the transport mechanisms. The results showed that GT decreased the transport of NPs and the presence of DEHP decreased it further. Van der Waals forces and small electrostatic interactions coexisted between the PSNPs and GT and caused deposition. Ligand exchange caused greater deposition of PSNPs−COOH on GT-coated sand than that of PSNPs. Although hydrogen bonding existed between the DEHP and NPs with functional groups, an increase in the positive charge and chemical heterogeneity of the collector was the main reason for DEHP promoting the deposition of NPs. Because of low absolute negative zeta potential values, PSNPs−NH2 was sensitive to chemical heterogeneity, and thus fully deposited (over 96.9%) in GT and GT-DEHP-coated columns. Generally, the deposition of NPs due to chemical heterogeneity was more significant than that due to the formation of chemical bonds and van der Waals, electrostatic, and hydrogen interactions. Our results highlight that the surface charge and functional groups significantly influence the transport behaviors of NPs and elucidate the fate of NPs in the terrestrial environment.