Currently 177 vascular plant species are known or presumed to be obligately associated with water in Peru. Their composition and diversity were surveyed in relationship to their distributions among the natural regions of Peru. Despite considerable aridity, the coastal plains of Peru have important aquatic ecosystems, including marshes in river deltas and mangroves in the far north, near the border with Ecuador; 70 species of aquatic plants are found in this coastal region. The Andean highlands include a great variety of wetlands, plus lakes and rivers; 62 species are found, including eight species of Isoetes, some of which are potentially threatened by extinction. The Amazon region of Peru includes both steep montane rivers in the headwaters and wide floodplains formed by meandering rivers in the lowlands; 102 species are found distributed among these ecosystems, although many additional species are semi-aquatic. Research and conservation strategies for Peru's aquatic plants need to take into account these important regional differences.