In this study we evaluated the effects of changes in salinity, temperature, pH and dissolved oxygen on the spatiotemporal variation of zooplankton. Samples were collected in January−March, May; October−December 2010; and January−March 2011 in the Araruama lagoon, state of Rio de Janeiro, Brazil. There were eight fixed stations sampled using a WP2 net equipped with a flow meter. The zooplankton diversity of the Araruama lagoon was low and dominated by Cirripedia larvae and by the copepod Acartia tonsa, which is an indicator species of eutrophication. In general, a few species from the Cabo Frio region were able to adapt to the conditions of this hypersaline lagoon. In addition, a specimen of Monstrilla bahiana (Monstrilloidae) was found at a salinity of 46‰. This is the first record of the order Monstrilloida in the region of Cabo Frio. Temperature, salinity and pH were shown to be limiting factors for the species present in the lagoon since Cirripedia seemed to avoid releasing their larvae under unfavorable environmental conditions. The abundance of A. tonsa was always associated with that of Cirripedia larvae, and it was higher at cooler temperatures.