All three species of file snake are aquatic and appear to be nocturnal. Nighttime activity seems related largely to foraging, and snakes have been observed patrolling shallow tidal pools, where fish tend to become concentrated. During daylight hours these snakes are very reclusive, hiding among tangled mangrove roots, river edges, or in holes and burrows. In captivity, these snakes bury themselves in mud. Java file snakes have been observed to burrow in riverbanks beneath the roots of trees, where they are sometimes found in large aggregations. Java file snakes are occasionally seen swimming, mostly because of the periodic need to breathe air at the water's surface. Although they are adept swimmers, file snakes often move by crawling sluggishly over muddy substrates at the bottom of streams or swamps. Younger, smaller snakes are seldom seen, and very little is known about their ecology.

Although movements of file snakes are generally described as sluggish, data on the Arafura file snake indicate these snakes sometimes make extensive daily excursions. Occasional specimens of the little file snake have been found on tidal mud flats, and it seems likely that file snakes might occasionally leave water to travel between bodies of water during times of tidal or seasonal fluctuation of water level. In at least some instances, however, file snakes are known to remain within a limited area year after year. Because file snakes have low energy requirements and exist in areas where fishes tend to be concentrated, population densities may be very high and are reported to be at least 100 snakes for every 2 acres (1 hectare) in some Australian billabongs.

Little is known about predation on file snakes. They may be eaten by crocodiles, various birds, and other animals and be captured by humans. It seems likely that the physiological and behavioral adaptations for prolonged submergence are related to avoidance of predation in shallow-water habitats.

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