Biocrusts are biological communities that occupy the soil surface, accumulate organic matter and mineral particles and hence strongly affect the properties of the soils they cover. Moreover, by affecting water repellency, biocrusts may cause a preferential infiltration of rainwater, with a high impact on the formation of local water pathways, especially for sand dunes. The aim of this study is to shed light on the connections between water repellency and pH, carbonate and organic matter content in two dune ecosystems with different biocrust types. For this, we used contact angle measurements, gas volumetric carbonate determination and organic matter characterization via FT-IR and TOF-SIMS. In both ecosystems, moss-dominated biocrusts showed higher water repellency and higher amounts of organic matter compared to algal or cyanobacterial biocrusts. Surprisingly, the biocrusts of the two dune systems did not show differences in organic matter composition or organic coatings of the mineral grains. Biocrusts on the more acidic dunes showed a significantly higher level of water repellency as compared to higher carbonate containing dunes. We conclude that the driving factor for the increase in water repellency between cyanobacterial and moss-dominated biocrusts within one study site is the content of organic matter. However, when comparing the different study sites, we found that higher amounts of carbonate reduced biocrust water repellency.