The smallest species, the little file snake, is primarily marine but tolerates water of varying salinity, including freshwater. These snakes are found in the sea but live more typically in mangroves or other areas of shallow coastal waters, including estuaries. Little file snakes have been captured at depths of 13-66 ft (4-20 m) as far as 1-6 mi (2-10 km) offshore, but shallow waters of a few feet (meters) or less are more typical of primary habitat. Populations enter rivers throughout the range, and a few populations are known to live in freshwater lakes in Papua New Guinea and the Philippines. The inland distribution of this species is probably limited by waterfalls rather than by lack of tolerance for freshwater.

The Java file snake is largely an inhabitant of lagoons and streams as well as other areas of permanent freshwater. The species also enters estuaries and the sea, but permanent occupation of marine habitats is unlikely. The Java file snake should be considered a freshwater species.

The Arafura file snake is a freshwater species that occupies tropical rivers and billabongs (dry streambeds that fill only seasonally), reaching high population densities in some of the drainage systems of northern Australia. Much of this habitat is subject to periodic fluctuation in water level caused by seasonal aridity in parts of the range. The snakes live in billabongs during the dry season but disperse into inundated grassland with the onset of wet-season flooding.

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