Zooplankton community composition, biomass and metabolism can vary drastically over space and time in subtropical estuaries. Changing environmental conditions can affect communities differently, depending on the characteristics of the species involved. In the present study, we compared the rates of oxygen consumption of the dominant zooplankton taxa living in permanently open and in temporally open/closed estuaries. The metabolic response was tested at four temperatures experienced by the animals in their natural environment. Zooplankton from the temporally open/closed estuary showed low activation energies and low rate of metabolism at the highest temperature tested. Animals from the permanently open estuary had higher respiration rates at increased temperatures than those from the open/closed counterpart, with one taxon showing a particularly strong response to temperature increase. Results suggest that the metabolism of zooplankton in subtropical estuaries can be influenced by the environmental conditions experienced and those characteristics need to be accounted for in the development of bioenergetics budgets of species and ecosystems.