In the European Union, assessments of the quality of the aquatic environment based on aquatic invertebrates are mandatory. Biological methods are supplemented with hydromorphological assessments of watercourses. There are many studies analysing the relationships between aquatic invertebrates and the hydromorphological assessment of the environment by the River Habitat Survey (RHS) method, but thus far, there has been no detailed study including water mites (Acari, Hydrachnidia) and the application of this method. In the present study, the following research hypothesis was put forth: a hydromorphological characterization of habitats is a significant element explaining the nature of water mite communities, and the RHS method can be used to predict the characteristics of Hydrachnidia populations in a river. The research was carried out in a small lowland river, the River Krąpiel (north-western Poland). Six locations were selected as representative of some state of habitat modification for the assessment of the hydromorphological conditions of the river and the collection of biological samples. The following conclusions can be drawn from the research: (1) the biology and ecology of water mites make them suitable as bioindicators of the environment, including hydromorphological modifications, and (2) the hydromorphological characteristics of habitats explain the nature of water mite communities in the river at the level of general population parameters (number of specimens and species), while at the species level, general regularities in water mite fauna distribution in river ecosystems, the continuity of the river ecosystem, and characteristics at a smaller spatial scale (habitat scale) better explain water mite community structure than the hydromorphological indices determined for a given site or section of the river.