The abundance and spatial distribution of zooplankton at monthly intervals were studied in polluted Golden Horn Estuary (Istanbul, Turkey), from July 2006 to December 2007. Selected water quality parameters also were measured. The zooplankton community was characterized by the presence of freshwater, estuarine and marine species, with a total of 59 taxa. Rotifers were the most important fraction of the total zooplankton, comprising 36.52% of all the samples. The zooplankton exhibited seasonal patterns, with the highest abundance occurring in the summer (979 ind. L À1 ) and the lowest in the spring (856 ind. L À1 ). Rotifera was the most abundant group in the upper and middle estuary, whereas Copepoda usually reaches the maximum densities in the higher salinity waters in the lower estuary. The study results indicated that both the sampling time (seasons) and sampling sites jointly had significant effects on the zooplankton densities (MANOVA P < 0.05), and horizontal patterns were related to electrical conductivity, water temperature, dissolved oxygen, suspended particulate matter, pH and chlorophyll a measured in the estuary.This study is part of the PhD thesis of Zeynep Dorak, titled 'Influences of abiotic factors on seasonal changes of zooplankton in Golden Horn, Istanbul, Turkey'.