Abstract The aim of the study was to compare the biological analyzes of the Linda River (Central Poland), which were based on three diatom indices: IO, GDI and IPS in order to select the best diatom index for the biological assessment of the lotic water quality. Additionally, the summary of the selected results of the biological and chemical analyzes was presented to show how precise the biological analyzes are as a basic tool in the assessment of the ecological status of the lotic waters. The results showed that each of the indices assessed the water in the Linda River to a specific but different quality class. The IO index showed class II of the water quality, while the IPS and GDI — class III. Statistical analysis conducted with the nonparametric Kruskal-Wallis test for independent samples (Kruskal, Wallis 1952) showed that differences in the values of individual indices at different sites were not statistically significant. It should be noticed that the IPS and GDI indices gave values that classify the water in the Linda River at least one class below. The obtained results confirmed that the biological methods are most reliable in the assessment of the water quality. These methods are less sensitive to a single impact of the environmental factors, therefore they permit accurate determination of the ecological status of the water ecosystems.