During 1997–1999, Conservation International conducted a survey of the coral reef in the area. According to the survey, the coral diversity is relatively low, but fish species variation is rich. Some species found during the survey include Pogonoperca ocellata, Chaetodon gardneri, Chaetodon xanthocephalus, Centropyge flavipectoralis, Genicanthus caudovittatus, Halichoeres cosmetus, Stethojulis albovittatus, Scarus enneacanthus, Scarus scaber and Zebrasoma desjardinii.
On 13 March 2004, a specimen of the rare and unusual species of shark, megamouth shark, was washed ashore on Gapang beach. Megamouth shark has a distinctive large mouth, very short snout and is broadly rounded in dorsal view. The specimen is said to be the 21st (some say it is the 23rd) sighting of the species since its discovery in 1976. The male shark, measuring 1.7 metres (5.6 ft) in length and weighing 13.82 kg (30.5 pounds), was frozen and sent to the Indonesian Institute of Sciences (LIPI) for further scientific study. As of 2006, there have only been 36 findings of megamouth sharks in the Pacific, Indian and Atlantic oceans.
The 2004 earthquake and tsunami has affected the island's ecosystem. At Iboih village, a large swath of mangrove was destroyed. Debris from the land was deposited on the nearby reefs as a result of the tsunami. In 2005, about 14,400 mangrove seedlings were replanted to save the mangrove forest.
Apart from underwater ecosystem, Weh island is the only habitat of one threatened species of toad, named Bufo valhallae (genus Bufo). The species is only known from the holotype from the island. Due to heavily degraded forestation on the island, the population of the species is uncertain.
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