The present work investigates the impact of site management on the retention of organic compounds in soil in a long-term field experiment and focuses on the role of particle size fractions. Specifically, we studied the influence of long-term farming practices on the soil's ability to adsorb five hydrophobic organic compounds (HOCs), specifically naphthalene derivatives (naphthalene, 1-naphthol, 1-naphthylamine, 1-hydroxy-2-naphthoic acid, 1,4-naphthoquinone). We examined the sorption on soil and its particle-size fractions with varying amounts and origins of organic matter in soil amended with farmyard manure and mineral fertilizers over more than 40 years. The soil organic matter had no significant impact on the sorption behaviour of the HOCs. Adsorption on the clay and silt fraction provided a deeper insight into the mechanisms and indicates a strong affinity with adsorption sites of the mineral phase. Naphthalene derivatives with hydrogen atoms in their functional groups adsorbed more strongly than other compounds on to soils containing smaller amounts of organic carbon. Desorption experiments with five organic extractants showed partitioning models for HOCs between extractant and soil surface. Only in experiments with the most polar extractant, formamide, did we observe an influence of the compound's functional groups on the desorption mechanisms. Column experiments with a HPLC-system and on-line UV-detection proved to be a satisfactory alternative to batch experiments. This approach should enable investigations of adsorption with larger numbers of compounds and soils at the same time.