Progressing climate change increases the frequency of droughts and the risk of the occurrence of forest fires with an increasing range and a dramatic course. The availability of water and its movement within an ecosystem is a fundamental control of biological activity and physical properties, influencing many climatic processes, whereas soil water repellency (SWR) is a key phenomenon affecting water infiltration into the soil system. Focusing on wide-spectrum effects of fire on the soil system, the research was conducted on a pine stand (Peucedano-Pinetum W. Mat. (1962) 1973) in Kampinos National Park located in central Poland, affected by severe and weak fires, as well as control plots. The main aim of the study was to examine the regeneration of the ecosystem 28 months after the occurrence of a fire. The effect of SWR and soil moisture content, total organic carbon, nitrogen and pH, and gain an understanding of the environmental conditions and processes that shaped the evolution of the species structure of soil microorganism communities (fungal vs. bacterial) have been examined. The Water Drop Penetration Time (WDPT) test was used to assess spatial variability of SWR in 28 plots. Soil bacterial and fungal communities were analysed by Illumina’MISeq using 16S rRNA and Internal Transcribed Spacers 1 (ITS1) regions in six selected plots. After a relatively wet summer, elevated hydrophobicity occurred in areas affected by a weak fire as much as 20 cm into the soil depth. The severe fire and subsequent increase in the richness of the succession of non-forest species contributed to the elimination of hydrophobicity. SWR was more closely linked to the structure and diversity of soil microbial communities than soil physicochemical properties that took place in response to the fire. A statistically significant relationship between the relative occurrence of microorganisms (≥ 1.0% in at least one of the samples) and SWR was established for the following fungi and bacteria species: Archaeorhizomyces sp., Leotiomycetes sp., Byssonectria fusispora, Russula vesca, Geminibasidium sp., family Isosphaeraceae and Cyanobacteria (class 4C0d-2, order MLE1-12). Insight into the functional roles of the individual identified microbial taxa that may be responsible for the occurrence of hydrophobicity was also presented.