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 (biochar_DOM (BC_DOM), wheat straw_DOM (WS_DOM), and swine manure_DOM (SM_DOM)) 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, SM_DOM exhibited the highest retardation of 50NPs transport and promoting effect on 400NPs transport. Owing to a high HIX, the effect of BC_DOM on the mobility of 400NPs was higher than that of WS_DOM. However, high cellulose content in WS_DOM caused it to exhibit a 50NPs retardation ability that was similar to that of BC_DOM. 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.