Populations of Moina micrura and Brachionus rubens in a deep waste treatment pond were exposed to the natural short-term fluctuations of unionised ammonia (90-min intervals of monitoring) that occur in the course of a day during a summer algal bloom. Under natural conditions, three replicate experiments were conducted in which water temperature, pH, dissolved oxygen, total ammonia, unionised ammonia, phytoplankton biomass and zooplankton (number of living and dead organisms, mortality rate and instant mortality) were studied. The time-course of unionised ammonia concentration was consistent with those shown by temperature, pH, phytoplankton biomass, dissolved oxygen, Moina micrura mortality and Brachionus rubens mortality. On the other hand, temperature, pH and dissolved oxygen never exceeded the tolerance ranges described for Moina and Brachionus, which led us to attribute the cause of zooplankton mortality to unionised ammonia toxicity. Mortality rates of 63%, 27% and 34% were recorded for Moina in each replicate experiment. Brachionus was less affected, with mortalities of 7.3%, 6.2% and 6.0%. These results confirm previous field observations (Water Res. 34(14) (2000) 3666; Water Res. 37(5) (2003) 1048) that attributed a reduction in zooplankton biomass during certain periods of summer (algal blooms) to a harmful side-effect of an excessive increase in phytoplankton biomass: high photosynthetic activity during these periods of proliferation of algae gives rise to an increased pH (>/=8) and, subsequently, leads to production of unionised ammonia (toxic for aquatic organisms) from its ionised fraction.