The comet assay method is a research technique for detecting damage to cellular DNA due to active physical or chemical agents. The comet assay is based on electrophoretic migration of genetic material contained in the cell’s nucleus. This research method is commonly used in many different fields, such as toxicology, environmental protection, and pharmacology. In recent years, the comet assay has attracted considerable attention from scientists studying the effects of harmful substances on the genetic material in the cell’s nucleus. The presence of pesticides in the environment is a threat to animals, because of the negative effects of pesticides on cells and their genetic material. Therefore, the aim of this paper, based on the available literature, was to describe the use of the comet assay in assessing the genotoxicity of pesticides to cells of aquatic organisms, as well as to describe the methodology and potential complications of this procedure.