Palaeobotany applied to freshwater plants is an emerging field of palaeontology. Hydrophytic plants reveal evolutionary trends of their own, clearly distinct from those of the terrestrial and marine flora. During the Precambrian, two groups stand out in the fossil record of freshwater plants: the Cyanobacteria (stromatolites) in benthic environments and the prasinophytes (leiosphaeridian acritarchs) in transitional planktonic environments. During the Palaeozoic, green algae (Chlorococcales, Zygnematales, charophytes and some extinct groups) radiated and developed the widest range of morphostructural patterns known for these groups. Between the Permian and Early Cretaceous, charophytes dominated macrophytic associations, with the consequence that over tens of millions of years, freshwater flora bypassed the dominance of vascular plants on land. During the Early Cretaceous, global extension of the freshwater environments is associated with diversification of the flora, including new charophyte families and the appearance of aquatic angiosperms and ferns for the first time. Mesozoic planktonic assemblages retained their ancestral composition that was dominated by coenobial Chlorococcales, until the appearance of freshwater dinoflagellates in the Early Cretaceous. In the Late Cretaceous, freshwater angiosperms dominated almost all macrophytic communities worldwide. The Tertiary was characterised by the diversification of additional angiosperm and aquatic fern lineages, which resulted in the first differentiation of aquatic plant biogeoprovinces. Phytoplankton also diversified during the Eocene with the development of freshwater diatoms and chrysophytes. Diatoms, which were exclusively marine during tens of millions of years, were dominant over the Chlorococcales during Neogene and in later assemblages. During the Quaternary, aquatic plant communities suffered from the effects of eutrophication, paludification and acidification, which were the result of the combined impact of glaciation and anthropogenic disturbance.