The paper aims to assess potential soil water repellency (SWR) in the surface layers of long-term agricultural fen soils. Furthermore, we attempt to enhance our understanding of the links between selected soil properties (e.g., secondary transformation, total organic carbon (TOC) content) and SWR in differently used (grasslands and arable lands) fen soils in the temperate climate zone. The study was conducted in the Grójec Valley, Central Poland. The soil samples for laboratory analyses were collected in June 2022 from 64 sampling points – 56 grassland and 8 arable sites. We found that secondary soil transformation (mursh forming process) was significantly positively correlated with SWR – determined by MED (molarity of ethanol droplet) and WDPT (water drop penetration time) methods (r = 0.42 and r = 0.40, p < 0.05) only in the organic samples (i.e., mursh). The significant positive correlation between SWR and TOC content (r = 0.73 (MED) and r = 0.74 (WDPT), p < 0.05) indicates that, as well as organic matter depletion, there was a decrease in the water repellency of the studied soils. Our results indicate that study fen sites should be rewetted, and that the implementation of the paludiculture must take place in the near future. At a minimum, further arable cultivation of organic soils should be avoided, as they are the most vulnerable to secondary transformation and exhibit high SWR values. Furthermore, in the case of crop production on post-organic soils, it is recommended that the conservation tillage method is applied to prevent further depletion of soil organic matter content.