Modern biodiversity research focuses on multiple diversity facets because different indices may describe different ecological and environmental processes, as well as the effects of varied disturbances of natural and anthropogenic origins. We investigated littoral macroinvertebrate diversity in a large boreal lake system and specifically explored congruence of indices within and between the three diversity facets: species diversity, functional diversity and taxonomic distinctness. First, we found that the indices of taxonomic distinctness were the most sensitive indicators of eutrophication. Second, we observed that most correlations between the indices within the same diversity facet, and between the indices of functional and species diversity, were relatively strong. However, the indices of taxonomic distinctness (Δ+ and Λ+) were weakly associated with other metrics of diversity, emphasising the importance of taxonomic distinctness as a complementary dimension of biodiversity. Therefore, our observations support the importance to examine multiple facets for mapping biodiversity or for assessing the effects of anthropogenic disturbances on biological communities.