The Antarctic Peninsula is one of the Earth’s most rapidly warming regions, which alters the natural seasonal cycles. Every year, the increase in temperature and solar radiation during spring/summer support the occurrence of phytoplankton blooms, which are the foundations of the high productivity of Antarctic seawater systems. Chile Bay, (Greenwich Island, South Shetlands) is a relatively closed bay influenced by freshwater from sea ice melting and surrounding ancient glaciers. In the present study, the diversity and composition of phyto- and bacterioplankton communities were studied during two consecutive but contrasting summers. Meteorological conditions during summer 2013 were milder in terms of wind, precipitation and temperature. Low chlorophyll a content and phytoplankton abundance were found in 2013. In contrast, summer 2014 was sampled during an ascendant phytoplankton bloom. Bacterioplankton communities in these two contrasting scenarios were highly different, with only few operational taxonomic units shared between both summers. Summer 2013 was largely dominated by Alteromonadales, mainly Pseudoalteromonadaceae and Colwelliaceae, whereas 2014 was composed by a more diverse community of members belonging to Proteobacteria and Bacteroidetes phyla. Community structure and composition differences were probably due to the nutrient input by the phytoplankton. Network analyses also evidenced an increment in the community complexity during summer 2014, with higher interconnectivity among eukaryotic and bacteriplankton nodes in its network compared to 2013 that presented a higher modularity. Overall, summer phytoplankton blooms strongly influence the bacterioplankton community structure and composition in Antarctic Peninsula coastal waters like those in Chile Bay, and the accelerated climate changes can have a strong impact on that seasonal components interconnection with unknown repercussions for the food chain in Polar Regions.