In this study, variation in the bacterioplankton community structure of three Antarctic lakes of different nutrient status, was determined in relation to physical and chemical gradients at depth and at time intervals, across the seasonal transition from winter ice-cover to the summer ice-free period. The three lakes studied were: Moss Lake (low nutrient, with typical nutrient concentrations of 80 μg l−1 nitrate and 10 μg l−1 dissolved reactive phosphate), Sombre Lake (low nutrient, but becoming progressively enriched, with typical nutrient concentrations of 185 μg l−1 nitrate and 7 μg l−1 dissolved reactive phosphate) and Heywood Lake (enriched, with typical nutrient concentrations of 1180 μg l−1 nitrate and 124 μg l−1 dissolved reactive phosphate). Bacterioplankton community structure was determined using a combination of PCR amplification of 16S rRNA gene fragments and denaturing gradient gel electrophoresis (DGGE). Results indicated marked changes in this bacterioplankton community structure, which were particularly associated with the transition period. However, significant changes also occurred during the period of holomixis. Comparison of the results from lakes of different nutrient status suggest that increased levels of nutrient input, and in the timing and duration of ice cover will lead to marked changes in the structure and stability of the bacterioplankton community at existing levels of environmental change.