The main goal of the study was to recognize the mechanisms underlying assemblage structuring of aquatic beetle fauna inhabiting a medium-sized, lowland river exposed to anthropogenic pressures. An attempt was made to identify the impact of numerous abiotic factors on how beetle communities are formed, with particular emphasis on geomorphological and landscape-related factors, which tend to be omitted from many studies of aquatic organisms. Our intention was to refer the results of our study to the general assumptions of the River Continuum Concept. Field studies were conducted in 2010, at 13 sites located along the Krąpiel River (north-western Poland). In total, 3,269 beetles were captured, representing 120 species and five ecological groups: crenophiles, rheophiles, rheobionts, stagnobionts a and stagnobionts b, which differ in environmental preferences. The core of the identified fauna was composed of stagnobionts, while rheophiles and rheobionts accounted for only 20% of the entire collected material. The formation of beetle assemblages was affected both by local factors, with an impact on aquatic environments, and by geomorphological factors, influencing a larger catchment. This was reflected in the high degree of conformity between dendrograms presenting similarities in the fauna at the studied sites, including the clustering of sites based on the abiotic factors that differentiated these sites. The presence of buffer zones, surfaces of patches denoted as “marshes” (marshland surface), “shrubs” (shrub surface), and “forests” (forest surface), and the distance to those patches seem to be the most important landscape factors affecting beetle communities. Of the factors influencing the aquatic environment, the following exerted the strongest effect: insolation, vegetation cover, presence of organic matter and BOD5, and anthropogenic pressure. The changes in assemblages of beetles determined in our study in the particular sections of the river course were a consequence of the effects of both internal factors and external ones, originating from the entire river’s catchment, which is in accord with the basic assumptions of the RCC.