Zooplankton distribution in the Bahia Callao, a low oxygen bay in Central Peru, was studied during surveys in March (austral summer) and September (austral spring) 2006. In March temperature was higher, but oxygen concentrations were much lower, especially near the sea floor. Zooplankton abundance at 14 repeated stations (March/September = 457/2356 ind. m−3), taxa number (35/97), and community composition changed drastically, but Acartia tonsa was dominant during both surveys. In contrast, abundance of meroplanktonic larvae did not change. The reproductive activity of A. tonsa was studied bi-weekly from November 2005 to August 2007 at a fixed station close to shore (9 m water depth). Population egg production rate ranged from 0.9 to 12.6 eggs female−1d−1 and was significantly related to Chlorophyll a, temperature, and dissolved oxygen. Individual clutch size ranged from 1 to 43 eggs. Egg hatching rate varied from 3.4 to 100%; the lowest values were associated with very low concentrations of dissolved oxygen in the surface layer and red tides. In feeding experiments at saturated oxygen concentrations >30 eggs female−1d−1 were produced, indicating continuous inhibition of egg production in the field. Oceanographic data demonstrate that the bay, and probably also the adjacent shelves, are exposed to frequent environmental changes, which challenge the survival and production of zooplankton and fish. The relationship between seemingly adverse environmental conditions and high biological productivity still needs to be understood.