Micro- and mesozooplankton were studied in the Sergipe estuary, northeastern Brazil, in order to assess the temporal variability in abundance and biodiversity under stressed conditions (urban pollution). Zooplankton samples and abiotic data were collected at one station during a full tidal cycle in July 2001 and in February 2002, corresponding to the rainy and dry seasons, respectively. The salinity regime was euhaline-polyhaline. Phosphate and dissolved oxygen were higher in July 2001, and nitrite, nitrate and ammonia in February 2002. Chlorophyll-a concentrations were low as a result of light limitation, with 1.18 +/- 0.88 microg x m(-3) in February and 1.53 +/- 1.48 microg x m(-3) in July. Fifty-nine zooplankton taxa were identified. Microzooplankton were abundant, mainly the tintinnid Favella ehrenbergii, and ranged from 18,649 ind x m(-3) in July to 678,009 ind x m(-3) in February. Mesozooplankton ranged from 1,537 ind x m(-3) in July to 37,062 ind x m(-3) in February and were dominated by barnacle nauplii in July and by copepods in February. The cluster analysis by taxa revealed the existence of three distinct groups: resilient species, characteristic of estuarine areas and occurring during all the year; species mainly more abundant in July (indicators of a healthier environmental condition); and species more abundant in February (tolerant to poor water quality).