The Araguaia River basin runs through the states of Goiás, Mato Grosso, Tocantins, and Pará, covering 373,000 Km2, mostly within the Brazilian Cerrado. The region has a wide variety of wetlands. The climate is characterized by high temperatures and strongly seasonal precipitation. There are two well defined seasons: the dry season (winter-spring) and the rainy season (summer- fall). The Araguaia River basin is dominated by plinthosoils that are found in low flat areas, poorly drained and prone to flooding, yielding wetland habitats of high plant diversity. Since the 1970s, human activities have led to reduction in both the diversity and area of wetlands. The construction of the Belém-Brasília highway and hydroelectric dams, as well as the expansion of agricultural and mining activities, have had major impacts on the region. The flora diversity data of the Araguaia River basin was developed through field work, herbarium research, and use of a database (Species Link). The resulting checklist of 162 aquatic and marshy monocotyledons from the Araguaia River basin represents 20 families and 50 genera. Cyperaceae (51 spp.), Poaceae (39 spp.), and Eriocaulaceae (16 spp.) are the most representative families. Life form analysis indicates that helophytes predominate (98 spp.; 60.5%). One hundred one species are native to tropical and/or subtropical America and twenty one are endemic to Brazil. Ninety-three species are new occurrences for the Araguaia River basin. Among them, three species are reported in the Brazilian Cerrado for the first time. This work contributes to the understanding of aquatic plant diversity in the Cerrado and other savanna-like vegetation physiognomies; environments and habitats poorly understood taxonomically and undercollected generally.