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The Prince Edward Islands (PEIs) lie within the Antarctic Circumpolar Current (ACC), in a transition zone bordered by the sub‐Antarctic Front (SAF) to the north and the Antarctic Polar Front (APF) in the south. A climate‐driven southward shift of the ACC and its frontal systems, the SAF and APF, in the vicinity of the PEIs is associated with a long‐term decline in the frequency of island‐associated phytoplankton blooms. These oceanographic perturbations coincide with significant declines in top predator populations attributed to shifts in the distribution and availability of prey, illustrating the interconnectedness between the marine and terrestrial ecosystems of the PEIs. This study investigated the influence of oceanographic variability on the marine ecosystem of the PEIs. A shift in phytoplankton and bacterial communities was observed that coincides with the position of the southern branch of the SAF, which was located to the north of the PEIs during 2014 and to the south during 2012, 2013, and 2015. These shifts in the diversity and structure of marine microbial communities correlate with significant perturbations in the position of the SAF relative to the islands leading us to conlclude that bacterial and phytoplankton communities in the PEI region are strongly influenced by shifts in the position of the SAF relative to the PEIs. This study highlights the critical need to link on‐going physical time series measurements with biological observations to provide a better understanding of the direct role that the upstream dynamics has on the near‐shore island environment and its productivity. [ABSTRACT FROM AUTHOR]