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Although forest vegetation predominates in the park, marshes, where grassy and shrubby vegetation is predominant, occur on the inside of river bends, at the ends of oxbow lakes, in channels that are in the process of closing, and at other places where recently deposited sediments are flooded by swift-moving water during the rainy season.

The marshes of Cantão hold a great diversity of plant life, and this becomes evident at the peak of the floods, when vines, shrubs, and floating vegetation flower, covering large areas with a mosaic of color. Most of these plants go on to produce fruit which are consumed by fish. In addition, broad mats of Paspalum repens grass and other floating vegetation with roots suspended in the current create a substrate for a very productive aquatic ecosystem. The roots of the vegetation are shaped so as to act like filters, trapping organic particles brought by the current, and doing so near the surface, where oxygen and sunlight are abundant. As a result, not only fish, but also fish predators like giant otters and the Black-collared Hawk move into the marshes to forage.

Marshes are also the prime breeding habitat for the park's abundant hoatzin population. The build their stick nests on the tops of isolated trees in the middle of the marshes, safe from terrestrial or arboreal predators. Many other species of bird also nest over marsh waters during the wet season, including the ubiquitous Great Kiskadee and the peculiar Greater Ani, which builds its communal nests in tangled vegetation over water.