This paper presents results on the spatial and temporal distribution patterns of mesozooplankton in the naturally fertilized region to the east of the Kerguelen Islands (Southern Ocean) visited at early bloom stage during the KEOPS2 survey (15 October to 20 November 2011). The aim of this study was to compare the zooplankton response in contrasted environments localized over the Kerguelen Plateau in waters of the east shelf and shelf edge and in productive oceanic deep waters characterized by conditions of complex circulation and rapidly changing phytoplankton biomass. The mesozooplankton community responded to the spring bloom earlier on the plateau than in the oceanic waters, where complex mesoscale circulation stimulated initial more or less ephemeral blooms before a broader bloom extension. Taxonomic compositions showed a high degree of similarity across the whole region, and the populations initially responded to spring bloom with a large production of larval forms increasing abundances, without biomass changes. Taxonomic composition and stable isotope ratios of size-fractionated zooplankton indicated the strong domination of herbivores, and the total zooplankton biomass values over the survey presented a significant correlation with the integrated chlorophyll concentrations in the mixed layer. The biomass stocks observed at the beginning of the KEOPS2 cruise were around 1.7 g C m−2 above the plateau and 1.2 g C m−2 in oceanic waters. Zooplankton biomass in oceanic waters remained on average below 2 g C m−2 over the study period, except for one station in the Polar Front zone (F-L), whereas zooplankton biomasses were around 4 g C m−2 on the plateau at the end of the survey. The most remarkable feature during the sampling period was the stronger increase in abundance in the oceanic waters (25 × 103 to 160 × 103 ind m−2) than on the plateau (25 × 103 to 90 × 103 ind m−2). The size structure and taxonomic distribution patterns revealed a cumulative contribution of various larval stages of dominant copepods and euphausiids particularly in the oceanic waters, with clearly identifiable stages of progress during a Lagrangian time series survey. The reproduction and early stage development of dominant species were sustained by mesoscale-related initial ephemeral blooms in oceanic waters, but growth was still food-limited and zooplankton biomass stagnated. In contrast, zooplankton abundance and biomass on the shelf were both in a growing phase, at slightly different rates, due to growth under sub-optimal conditions. Combined with our observations during the KEOPS1 survey (January–February 2005), the present results deliver a consistent understanding of patterns in mesozooplankton abundance and biomass from early spring to summer in the poorly documented oceanic region east of the Kerguelen Islands.