An important objective of aquatic ecotoxicology is to determine the effects of toxic compounds in organisms that play a central role in aquatic communities where rotifers have a large impact on several important ecological processes. The contribution of the rotifers to secondary production in many aquatic communities is substantial as they are often the larger fraction of zooplankton biomass at certain times of the year. In addition to the importance of their ecological roles in aquatic communities, the rotifers are attractive organisms for ecotoxicological studies by its short life cycles and rapid reproduction, their small size, and little volumes needed for culture and toxicity assays. The main end points used in ecotoxicological studies are mortality, reproduction, behavior, and biomarkers. Such parameters are included in international regulations from all over the world, where different species are used to evaluate the effect of environmental samples or chemical compounds. The high diversity of rotifers is an important issue because it can modify their relative susceptibility to toxicants. Thus, more studies are needed to know the relations and mechanisms involved in clonal variation, sensitivity, and development, which can be all assessed by state-of-the-art procedures.