In this review, we include rotifers, copepods, and cladocerans, including other groups not usually deemed as zooplankters: i.e., protists, acari, and large branchiopods. The objectives of this study were to integrate the dispersed literature on the taxonomy and diversity of these freshwater zooplankton groups and to explain (1) how these contributions can be arranged in distinct historical periods and (2) how this knowledge has allowed the detection of exotic and threatened species. We divided the freshwater zooplankton studies in Mexico into three historical periods: the first one comprised the 1840s to the 1940s when foreign researchers carried out most studies during several expeditions. Spanish researchers promoted surveys on different zooplankton taxa at the end of this first period. The second period, from the early 1950s to the end of the 1990s of the XX century, showed a remarkably increased research activity in its last ten years only (that is, during the 1990s to 2000), represented by contributions of a new generation of Mexican zooplanktologists. This period yielded more complete zooplankton listings and detailed morphological descriptions of rotifers, cladocerans, copepods, and large branchiopods. The third period started from the year 2000 to date. During this time, listings and online faunistic baselines based on integrative taxonomy have been the primary trend. An account of exotic zooplankters and conservation issues of several native species are discussed. The results of this review show that the knowledge of the freshwater zooplankton of this country has increased significantly over the last 40 years, with at least 408 first records of species for Mexico. Currently, the knowledge of Mexican freshwater zooplankton is among the most complete in the world. However, it is estimated that only a small fraction of the true diversity has been documented.