The transport of nanoplastics (NPs) through porous media is influenced by dissolved organic matter (DOM) released from agricultural organic inputs. Here, cotransport of NPs with three types of DOM (biocharDOM (BCDOM), wheat strawDOM (WSDOM), and swine manureDOM (SMDOM)) was investigated in saturated goethite (GT)-coated sand columns. The results showed that codeposition of 50 nm NPs (50NPs) with DOM occurred due to the formation of a GT-DOM-50NPs complex, while DOM loaded on GT-coated sand and 400 nm NPs (400NPs) aided 400NPs transport due to electrostatic repulsion. According to the quantum chemical calculation, humic acid and cellulose played a significant role in 50NPs retardation. Owing to its high concentration, moderate humification index (HIX), and cellulose content, SMDOM exhibited the highest retardation of 50NPs transport and promoting effect on 400NPs transport. Owing to a high HIX, the effect of BCDOM on the mobility of 400NPs was higher than that of WSDOM. However, high cellulose content in WSDOM caused it to exhibit a 50NPs retardation ability that was similar to that of BCDOM. Our results highlight the particle size selectivity and significant influence of DOM type on the transport of NPs and elucidate their quantum and colloidal chemical-interface mechanisms in a typical agricultural environment.