Metabolic diversity of heterotrophic bacterioplankton was tracked from early winter through spring with Biolog Ecoplates under the seasonally ice covered arctic shelf in the Canadian Arctic (Franklin Bay, Beaufort Sea). Samples were taken every 6 days from December 2003 to May 2004 at the surface, the halocline where a temperature inversion occurs, and at 200 m, close to the bottom. Despite the low nutrient levels and low chlorophyll a, suggesting oligotrophy in the winter surface waters, the number of substrates used (NSU) was greater than in spring, when chlorophyll a concentrations increased. Denaturing gradient gel electrophorisis analysis also indicated that the winter and spring bacterial communities were phylogenetically distinct, with several new bands appearing in spring. In spring, the bacterial community would have access to the freshly produced organic carbon from the early phytoplankton bloom and the growth of rapidly growing specialist phenotypes would be favoured. In contrast, in winter bacterioplankton consumed more complex organic matter originated during the previous year's phytoplankton production. At the other depths we tested the NSU was similar to that for the winter surface, with no seasonal pattern. Instead, bacterioplankton metabolism seemed to be influenced by resuspension, advection, and sedimentation events that contributed organic matter that enhanced bacterial metabolism.