Temporal changes in the structure of biological communities are one of the factors affecting water quality assessment systems. The aim of our work was to analyze the temporal variability of benthic macroinvertebrates and its consequences for the established streams typology. The data analyzed come from a biomonitoring of streams of the Czech Republic during 2002-2005. Changes of the structure of macroinvertebrates communities were observed using diversity indices (Shannon index) and biotic indices (saprobic index) and using actual changes in community structure. The time related shift in indices and the community composition was found, but the correlation of the locality typologies and the change was not found.