Organic matter effectively regulates nanoparticles transport. However, little is known about the effect of agricultural organic inputs on the transport of ferrihydrite nanoparticles (FHNPs) during aging. In this study, columns were filled with sand mixed with varying proportions of pristine, water-processing, or alkali-processing biochar or swine manure and used to simulate the release of organic matter and changes in surface roughness of sand grains during field aging. The influence of these factors on FHNPs transport was investigated using column experiments. The dissolved organic matter (DOM) (0.008–24.8 mg L−1) released from agricultural organic inputs decreased the zeta potential of the FHNPs from 30.8 mV to 14.6–-48.9 mV and further caused electrostatic repulsion, osmotic repulsion, and elastic-steric repulsion between FHNPs and mixed sand, thus enhancing FHNPs transport. Ferrihydrite nanoparticles transport increased with increasing content of biochar and swine manure due to the increased amount of DOM. However, with the presence of organic inputs, surface roughness up to a certain degree (the increase in specific surface area up to 4.6 m2) became the dominant inhibition factor affecting FHNPs transport. After DOM release, agricultural organic inputs decreased the enhancement of FHNPs transport; with the increase input, their rougher surface gradually increased inhibition of FHNPs transport. The strongest FHNPs retention in the alkali-processing biochar (0.2–10%) or swine manure (1–2%) mixed sand columns indicated that fully aged agricultural organic inputs strongly inhibited FHNPs transport. Our findings provided novel insights into the critical influence of agricultural organic inputs and their aging on FHNPs transport, which changed gradually from enhancement to inhibition gradually.