In this study, the zooplankton community and its relationship with environmental factors were investigated in the Karakaya Dam Lake (KDL). The physico-chemical characterization showed that there were obvious changes in the water quality and zooplankton population structure, which was mainly due to the organic matter source. Reactive phosphate (SRP) and nitrogen values were found in low concentrations. A total of 22 zooplankton taxa were determined, including 14 taxa of Rotifera, followed by 6 taxa of Cladocera and 2 taxa of Copepoda. The most abundant species were Synchaeta oblonga (Rotifera), Bosminia longirostris (Cladocera), and Cyclops scutifer (Copepoda). The abundance of zooplankton was highest in spring. Canonical correspondence analysis (CCA) was used to examine relationships between measured environmental variables and zooplankton composition. According to CCA, dissolved oxygen, and SRP values, there was a significant relation to zooplankton abundant with these factors. The triplots diagram demonstrated variations of the structure of zooplankton population composition which can be explained by the environmental variables. Oxidative stress (catalase, glutathione S-transferase, glutathione reductase) and neurotoxicity (acetyl cholinesterase) biomarkers were analyzed in copepod species. Glutathione reductase and acetyl cholinesterase activities were significantly inhibited in the summer. Catalase activity was induced in the spring. The seasonal changes of biomarker indicated that the KDL may be at risk of pollution that originated from agricultural and industrial activities.