Within the Mexico Megalopolis, there are wetlands of high hydrological, historical, cultural, and ecological value, yet their role has often been relegated in the face of urban and human demands. Knowledge of their aquatic flora is limited and even scarcer regarding the species that once inhabited the great lakes now covered by cities. The aim of this contribution is to provide a synthesis that broadens the perspective of the wetlands of the Megalopolis, considering them not only as water reserves, but also as functional and dynamic ecosystems that sustain a diversity of hydrophytes currently threatened by climate, water, and urban crises. In the region, 537 wetlands have been recognized, although only 34 have reports on their aquatic flora, equivalent to less than 7%. These environments, often small or seasonal, constitute biodiversity oases and are essential for numerous species. However, of the 23 Protected Natural Areas located within the Megalopolis, only 13 include wetlands with documented floristic richness, among them the Ciénegas de Lerma, the Xochimilco Canals, and Lake Texcoco, some of which are designated Ramsar Sites. In total, 270 records of aquatic, subaquatic, and tolerant plants were compiled, including 206 native species (five endemic) and five listed as threatened, such as Gentiana spathacea and Sagittaria macrophylla. These results reflect both the richness and vulnerability of the Megalopolis wetlands and highlight the urgent need to strengthen their study and conservation as key biodiversity refuges in central Mexico.