Rapid climate-driven melting of coastal glaciers may control plankton dynamics in the Western Antarctic Peninsula. It is known that in Potter Cove, 25 de Mayo/King George Island, phytoplankton is tightly coupled to meltwater input. However, no information on zooplankton is available in this regard. The aim of this study was therefore to examine the structure and dynamics of microzooplankton and mesozooplankton in two zones (the inner and outer Potter Cove) differently impacted by glacier melting during two contrasting austral summers (2010 and 2011). Microzooplankton composition differed between the two zones and years analyzed, and its total biomass was observed to be highest far from the glacier influence and during 2010. Mesozooplankton composition and biomass were similar in the two zones and years analyzed. Colder than usual conditions in the summer of 2010 prevented glacier melting, thus favoring the development of an exceptional micro-sized diatom bloom (~190 µg C l−1 and >15 µg l−1 chlorophyll a), which was tightly followed by a maximum in large copepod abundance. After the bloom and in coincidence with intense glacier melting, large diatoms and large copepods were observed to be replaced by nanophytoplankton and microzooplankton (aloricate ciliates and dinoflagellates), respectively. In 2011, low phytoplankton abundance, probably controlled by high tintinnid biomass, was observed as a result of warmer temperatures than 2010 and low-salinity waters. Large copepods appeared to have exerted a high grazing pressure on aloricate ciliates and heterotrophic dinoflagellates in 2011. Our results suggest that whereas the joint effect of water temperature, salinity and phytoplankton availability as well as composition could be of primary relevance in structuring micro- and mesozooplankton community, zooplankton could be of secondary relevance in controlling phytoplankton biomass in Potter Cove during the two summers analyzed.