[16] The ecology of the upper reaches of the river has been severely disrupted by excessive logging and clearing of land for plantations, although the original lowland forest and mangrove swamps near the coast have largely survived, providing sanctuary for a population of saltwater crocodiles (Crocodylus porosus) and containing some of Borneo's highest concentrations of wildlife.

[19] Much of the deeper river area is protected under the Lower Kinabatangan Sanctuary, a 28,000-hectare (69,190-acre) reserve established in 1999 that provides a variety of habitats for flora, especially a freshwater swamp forest, mangroves, palms, and bamboo, as well as fauna, such as Hose's langurs, proboscis monkeys, orangutans, pig-tailed macaques, gibbons, slow lorises, elephants, Sunda clouded leopards, and rhinoceros.

[19][20] Since the beginning of the modern era in the early 1950s until 1987, the lower Kinabatangan area has been subjected to commercial logging activities, and more than 60,000 hectares (148,263 acres) of its lowland rainforest have been developed into cocoa and palm oil plantations.

[21] In 2011, Nestlé launched a reforestation project of the riparian area along the Kinabatangan River in Sukau to create a landscape where people, nature, and agriculture activities could co-exist harmoniously in their need for water.

[22] Most nature tourism in the Kinabatangan River area is concentrated around Sukau since it is accessible by road and offers comfortable accommodation to visitors prepared to pay for well-managed tours.

A 350 m (1,150 ft) bridge linking Sukau with Litang and Tommanggong was planned but cancelled in April 2017 after opposition from conservationists, including David Attenborough, due to potential adverse effect on the local pygmy elephant population.