The application of organic fertilizers is a major anthropogenic input into an agricultural ecosystem. A possible effect on the transport to groundwater of a herbicide such as atrazine must be considered. Soil column experiments with the fitting of the breakthrough curves to a convection-dispersion transport model showed that the relative time of fertilizer application was important. When the fertilizer was applied before the herbicide, the resulting organic residue on the surface sorbed at least part of the atrazine and had slow release properties. The dispersion coefficient was significantly increased and the amount of atrazine in leachate significantly decreased. The application of fertilizer after the herbicide had no significant long-term effect but did significantly slow the initial leaching rate of the atrazine, suggesting that the interaction between the herbicide and the soil was temporarily enhanced by fresh material leaching out of the fertilizer. A mechanism to explain this 'negative' co-transport is proposed.