Determination of the relationships between environmental factors and diatom assemblages is usually made for several hundred lakes spread over a large area. However, the analysis of several lakes located near Lake Wigry also gives interesting results. Lakes in Wigry National Park (Poland) with broad similarity of geological origin show clear limnological, physical, and chemical differences. Here, we report on an investigation into how these dissimilarities influence diatom assemblages. Hierarchical Cluster Analysis showed that the studied lakes can be divided into three groups: (1) disharmonic, (2) harmonious with greater human impact on the environment, and (3) harmonious with a more limited human impact. The harmonious lakes could be divided into two groups that are mainly in line with the contents of the chloride and sulfates ions taken as indicative of human impacts on the environment. Overall, the three groups had different dominance structures, as reference to the Dominance Index (DI) made clear (mean values being: (1) −70.54%, (2) −72%, and (3) −54.58%, Generalized Linear Models with the categorical independent variable (group) showed significant differences between groups (for 1–3, 2–3) p value < 0.05). Lakes impacted by anthropopressure and disharmonic ones had the strongest dominance structure. More broadly, DI differences between the groups are consistent with the Species Pool Hypothesis (SPH), while studied differences can be said to result from natural geological dissimilarities, as well as disparate anthropogenic impacts.