Morphological alterations in zooplankton are induced by exposure to hazardous materials in the environment. These alterations in the body are excellent indicators of adverse effects at the (sub) individual and population levels. These changes might be undetectable within a population in the first generation; however, it was recently documented that alterations are more frequent in the subsequent generations. Because of this, we revised scientific literature that reported malformations in cladocerans, copepods, oligochaetes, and rotifers caused by diverse toxicants when organisms were exposed either in the laboratory or in natural conditions. From an environmental perspective, we focused on the importance of morphological alterations in zooplankton, the most likely causes, and their consequences. Furthermore, the present article shows that alterations of the normal morphology could be used as consistent biomarkers, but further research requires discriminating the influence of natural behavior and the consequences of exposure to toxic compounds.