Although there are some species of midwater shrimps that seldom if ever encounter the bottom of the ocean, the vast majority of decapods are associated with benthic habitats. Marine decapods live in all types of habitats from intertidal mud flats to deep-sea hot vents. Such highly structured habitats as rock or coral reefs, seagrass beds, and mangrove forests support the greatest numbers of species, but even featureless sand and mud bottoms support many types that are adept at burying themselves. Most decapods emerge to feed only at night when fewer predatory fishes are active.

Structures to hide in are also important for freshwater decapods; they are most abundant in vegetated areas. Many freshwater decapods construct burrows that allow them to remain in contact with ground water when their pond dries up. Terrestrial decapods are also dependent on water; while some crabs can occur as much as 9 mi (15 km) from the ocean and up to 3,280 ft (1,000 m) above sea level, they all have planktonic larvae and must return to the ocean to breed.

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