Vegetation changes according to habitat conditions, which vary considerably in Pantanal depending on whether or not the area is flooded and the length of time land is under water. For this reason there is a great variety in plant cover. There is a mosaic of aquatic communities, which may be submersed, floating or fixed on the muddy substrate and which may contain even mesophytes and xerophytes.

The so-called cordilheiras, covered by forests and cerrados, are never flooded, cattle and many wild animals seek shelter here during the rainy season. In flooded areas where the water is deep, there is a rich vegetation of hydrophytes, including a sub-species of the great vitória-régia (Victoria regia cruziana), In areas where the water flows more or less rapidly, there are immense grasslands, used as pasture by the large herds of cattle raised in Pantanal. Besides the grasses, there are many herbs from many botanical families, and islands of cerrados and semideciduous forests (whose leaves fall during a certain period of the year). Outcroppings of limestone rock in various places are locally known as serras. The vegetation here resembles the caatinga. Over vast areas, one species may dominate; this generate diverse types of vegetation such as cambarazal (Vochisia divergens), carandazal (Copernicia alba), piuval (Tabebuia sp), pirizal (Cyperus giganteus), tabual (Typha domingensis). There are no plants exclusive to Pantanal known at the present time.

Pantanal is a region in transformation. It is relatively new and unstable from a geological point of view and is dominated by a complex mixture of plants and communities. It lies at the border area of four floral provinces: Hylaea, Cerrado, Chaco, and southeastern Brazilian forest (Paraná province). The Pantanal plain (PP) is surrounded by bordering regions which can be divided as follows:

• Northwestern border area (NW): This sector can be described as Amazonian. In it cerrado is mixed with semideciduous forests which are marked by Amazonian floristic elements.
• Northeastern border area (NE): The northeastern sector is clearly dominated by cerrado. As in the NW sector, Amazonian-influenced semideciduous forests are present, although in smaller areas.
• Southeastern border area (SE): In the southeastern sector there are areas with cerrado and others with semideciduous forests which contain elements of the southeastern Brazilian Atlantic Forest (Mata Atlântica).
• Southwestern border area (SW): In the southwestern border area, elements of the Chaco, such as Copernicia palm forests, dominate as well as semideciduous and deciduous forest; in particularly dry places on limestone outcrops, elements of the Caatinga can be found.

A seasonal climate and high temperatures are essential in formation of tropical savannahs. During drought, the water shortage force the plants to develop survival strategies. The grasses dry up so that fires are common. During the rainy period, topographical conditions and soil different compositions decide whether rainfall is absorbed and stored or flows away on the surface to flat impermeable areas, causing flooding. The types of vegetation occurring in Pantanal are therefore closely related to the seasonality of climate and conditions of ground - and floodwater:

• Campo Sujo (open grassland): Brazilians use the term campo for various grassland types. Open grasslands occur naturally in the higher mountain ranges, often in regions with a shallow layer of topsoil on a rocky basement. Cerrado can be transformed into open grassland by frequent burning.
• Cerrado (scrubland): Brazilian designation for savannah. Enormous stretches of open grassy country with a more or less dense growth of bushes and low, often crookedly formed trees, are found in Central Brazil. Cerrado is usually found on well-drained, leached, acid soil which is poor in nutrients and has a high content of aluminum (Eiten,1972). Great part of cerrado's woody plants are endemics; they show a high degree of fire resistance as an adaptation to the frequent fires occurring in the Brazilian savannah regions. In the Pantanal plain, cerrado occurs in many places with sandy topsoil not reached by groundwater.
• Cerradão (dense woodland): Brazilian designation for savannah woodland. This type of forest has a closed trees canopy, but there is no distinct stratification in the tree-layers. The trees are 10-14 m high, often branching low in the middle third of the trunk and with a tendency to twisted growth. The ground cover consists of shrubs and often of many terrestrial bromeliads. Floristically, cerradão consists of a large number of tree species found in the cerrado as well.
• Evergreen Forest: Evergreen forest may occur in areas where the soil is fertile and the groundwater level does not show much fluctuation. Such conditions exist at the foot of mountain slopes, or along rivers in hilly areas. These forests may exist to a greater extent in Pantanal's northern border areas.
• Semideciduous Forest: This type of forest has an upper, often incomplete canopy, 18-24 m high. The trees of this storey are completely deciduous during the dry season. The lower storey is made up of mixed evergreen and deciduous trees, 8-10 m high. The ground cover consists of shrubs, palm seedlings, terrestrial bromeliads, and various herbaceous plants. Semideciduous forest generally grow on fertile soils; this type of forest has therefore been destroyed and transformed into pastures in large scale, especially in the northern border areas.
• Deciduous Forest: This type of forest can be found on hill slopes, especially on calcareous rocks. The trees and the shrubs of the undergrowth are completely deciduous during the arid months. Floristically this type of forest seems to be closely related with semideciduous forests.
• Gallery Forest of lowland rivers: Lowland rivers usually form river banks which lie 1-2 m higher than the surrounding floodplain. On these river banks, which are rarely flooded by highwater, semideciduous forest and/or cerradão may be found.
• Seasonally flooded woodland: This type of woodland commonly occurs on floodplains in the vicinity of major streams. There is usually a lower canopy formed by tall shrubs and low trees, with a few emerging higher trees. In its floristic composition this type of woodland is quite distinct from semideciduous forests and cerradão.
• Seasonally flooded grassland: This type of grassland, which in Portuguese may be called campo alagado, is classified as wet savannah; it is widespread in floodplains with impermeable soils which are flooded for long periods during the rainy season. It consists of Gramineae, Cyperaceae, Burmanniaceae, Scrophulariaceae, and other herbaceous plants together with a few woody plants such as Curatella americana, Bryrsonima orbignyana, Bactris glaucescens, and Licania parvifolia which can tolerate the double stress of seasonal drought and flooding.
• Forest Islands: Areas of forest of varying size from 10-15 m up to several hundred meters in diameter can also be found on patches of elevated ground in typical wet savannah. Usually these areas take the form of small woods, which are scattered about the flood savannah like islands. Measurements of these forest islands showed that their surfaces were higher than the surrounding wet savannah, sometimes by 40-60 cm but in extreme cases by as much as 140 cm. These mounds are therefore out of reach of the wet season floodwaters, so that trees can become established on them. Both trees of cerradão or semideciduous forest may be found; in many parts of Pantanal, Tabebuia heptaphylla is a typical tree species growing on these mounds. In the centre of these forest islands there is often a termite nest or, more rarely, a nest of leaf cutter ants. It seems probable that the biological influence of the termite or ant constructions produces these higher mounds in the landscape. The forest islands are important shelters for various animals foraging outside in the wet savannahs, and certainly play an important role in the distribution of forest animals and birds throughout the Pantanal plain.
• Swamps and pond margins: Permanently flooded marsh areas and the margins of freshwater ponds are usually covered with dense aquatic vegetation; shrubs and herbaceous plants may be rooted in the mud in shallow water.