The influence of long-term farming practices on the soil's behaviour to adsorb hydrophobic organic compounds (HOCs) over long times was investigated. Adsorption of five naphthalene derivatives (naphthalene, 1-naphthol, 1-naphthylamine, 1-hydroxy-2-naphthoic acid, 1,4-naphthoquinone) was examined on soils with varying amounts and origins of soil organic matter obtained after amendment with different organic materials over more than 40 years. Soil organic matter, pore sizes and aggregate stability were significantly altered influencing the adsorption behaviour of the soils. Samples of soil amended with peat having an organic carbon content of 3.4% sorbed naphthalene derivatives stronger than the soil treated with sewage sludge (2.6% C(org)). All other treatments, calcium nitrate, plots without nitrogen fertilizers, grassland, animal manure, green manure and the fallowed soil sorbed less and no significant difference was found between them although the organic carbon content ranged from 1.0% to 2.6%. Thus, a decrease of the carbon content of a soil does not necessarily imply a reduction of sorption capacities for hydrophobic compounds such as naphthalene derivatives. Furthermore, the importance of protonation of HOCs for the adsorption on soil surfaces was shown. Different polarities of electronic structures of HOCs distinctly influence their adsorption behaviour.