The edible-nest swiftlet (Aerodramus fuciphagus) is the reason Niah National Park exists in the form it does. This small grey-brown bird, barely 12 cm long and weighing 15 grams, constructs its nest entirely from strands of solidified saliva secreted from the enlarged salivary glands of breeding adults. These nests — dissolved in water and consumed as "bird's nest soup" — are among the most expensive food products in the world by weight, and they have been harvested from Niah's caves for at least 1,500 years as attested by Chinese trade records.

Swiftlets navigate the total darkness of the Great Cave by echolocation — producing rapid clicks in the 2–5 kHz range and interpreting the returning echoes. Their echolocation is relatively crude compared to bats: they can detect large objects but not the fine-grain obstacles that microchiropteran bats perceive. In the cave, they typically follow the cave walls and the direction of light from the cave mouth, reserving echolocation for the darkest central chambers. At dusk and dawn, watching the swiftlet flight columns spiralling in and out of the cave mouth is one of Niah's signature experiences.

The swiftlets nest in colonies on the cave ceiling, constructing their white, translucent nests in cup shapes approximately 6 cm across. A nest takes 35 days to complete and represents roughly 30–35 days of the bird's total saliva output. Licensed collectors harvest the nests using 60-metre rattan poles and bamboo scaffolding erected inside the cave — a tradition that predates the colonial era. The current management system attempts to balance harvest with conservation: collectors hold licensed concessions, and nests with eggs or chicks cannot be taken. In practice, enforcement is imperfect, and swiftlet populations in commercial caves have declined significantly across Borneo.

Inside Niah, swiftlet populations are protected within the national park boundary, though some licensed harvesting still occurs under heritage concession agreements. The most dramatic viewing opportunity is the evening exodus, when the wrinkle-lipped bat and swiftlet columns pass each other at the cave mouth in a coordinated exchange — bats pouring out as swiftlets stream in. This exchange happens 30–45 minutes after sunset and is visible from the cave mouth platform on the boardwalk trail.