In humid areas, biocrusts cover topsoils of inland dunes and influence soil characteristics, which, in turn, may affect the hydrophobicity of soils. The hydrophobicity of topsoils typically increases with increasing organic matter content. In addition, the soil organic matter quality, for example, described by the ratio of its hydrophilic and hydrophobic functional groups, also influences hydrophobicity. Because biocrust development goes along with an increase in the organic matter content and a shift in microbial community composition, the chemical character of soil organic matter likely changes over time, which, in turn, affects the hydrophobicity of the crusts. We hypothesize that the hydrophobicity of biocrusts increases during succession because of increasing amounts and aliphatic character of organic matter. We compared organic matter contents and Fourier‐transform infrared spectra of cyanobacterial biocrusts and moss‐dominated biocrusts at two European inland dunes. The organic carbon content as well as the hydrophobicity increased during crust development at both sites. Older moss‐dominated biocrusts showed the highest hydrophobicity and the highest organic carbon content. Moreover, at one study site, the hydrophobicity of the biocrusts did increase with decreasing ratio between hydrophilic and hydrophobic (i.e., aliphatic) moieties of soil organic matter. At the second study site, this effect was only visible for the moss‐dominated biocrust. We conclude that biocrust development and organic matter accumulation go ahead with changes in the organic matter composition and induce increased hydrophobicity with a strong impact on water redistribution in inland dune ecosystems. This knowledge will help to improve nature protection strategies in rare ecosystems.