The rivers flowing through Upper Silesia and the adjacent areas (Southern Poland) are affected by various anthropogenic pressures including urbanisation, agriculture and animal husbandry, as well as industry (e.g., mining), which are reflected in the measured physical and chemical water parameters. The species composition of rotifers relative to a variety of microhabitats was studied in eight small rivers of this region in 2017. Our research is a comprehensive and up-to-date analysis that focuses on the rotifers in small rivers and shows the diversity of rotifers relative to the microhabitats and environmental variables. The diversity of rotifers ranged from 0 to 23 taxa in individual samples. In the studied rivers, 129 taxa of rotifers were found. Notommata groenlandica, a species that has not been recorded in the country for 100 years, was found in two rivers. The Kruskal–Wallis one-way ANOVA and Dunn’s multiple comparison post hoc tests revealed statistically significant differences in the median number of rotifer taxa between the abiotic types of rivers, rivers, sampling sites, microhabitats and seasons. A multiple regression analysis revealed a significant relationship (correlation) between the number of rotifer taxa, and the concentration of nitrites, total dissolved solids and dissolved oxygen in the water.