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Bacterial populations rapidly turnover in both time and space, however, the composition and diversity of their communities in plankton and the dynamics of community changes have not been well investigated over longer time scales. We explored the dynamics of bacterial community composition (BCC) monthly over a seven year period from 2004 to 2010, within a large shallow eutrophic lake. Seasonal and year-to-year changes in BBC were assessed using a PCR-based 16S rDNA fingerprinting technique based on denaturing gradient gel electrophoresis (DGGE). The bacterial OTUs differed between ice-free and ice-covered periods and many recurred in specific seasons in consecutive years. The most significant variables related to within-year variation were temperature and the concentration of nutrients. Year-to year variability was larger compared to within-year variability. Therefore, variability tended to mask seasonal changes in BCC. The interannual differences in BCC were strongly related to abiotic conditions such as water level fluctuations that generally lead to water column mixing and sediment resuspension, and the qualitative composition of dissolved humic material. All highly related biotic variables that describe the total plankton community (in addition to bacteria including phyto-, protozoo- and metazooplankton) were found to be modulated primarily by changes in the abiotic environment.