Black stilts largely breed in the Mackenzie Basin in the South Island, and are threatened by introduced feral cats, ferrets, and hedgehogs as well as habitat degradation from hydroelectric dams, agriculture, and invasive weeds.

Black plumage may be an adaptation to "absorb heat better in the cold, windswept habitat of glacial riverbeds and lakeshores".

Although black stilts currently breed only in braided river systems in the South Island, subfossil bones show that prior to human arrival they were found in habitats as diverse as narrow bush streams in Hawkes Bay, and a wetland lake surrounded by forest in North Canterbury.

[9] Each year juvenile captive-bred birds are released into the wild along the Godley, Cass, and Tasman rivers in Te Manahuna/Mackenzie Basin, in August or September; 130 in 2019,[10] over 150 in 2021 and 143 in 2023.

[11][12] The annual release in the wild of captive-bred birds, combined with predator control, have probably prevented black stilt from becoming extinct.

In the 19th century, mustelids such as stoats, ferrets and weasels, as well as cats, were released into the Mackenzie Country to try to control the spread of rabbits.

[2] Compared with pied stilts, they have more noticeable plumage, are less likely to perform distraction displays while incubating, and their chicks take longer to fledge.

[2] Black stilts rely on wetlands and braided riverbeds for feeding, and these have been extensively drained or modified for agriculture, irrigation, and flood control.

[6] Invasive weeds such as Russell lupin and crack willow are able to colonise braided riverbeds, reducing nesting habitat and providing cover for predators.

[13] Artificial lowering of the level of Lake Benmore, which caused exposure of shallow riverbed in the deltas of the rivers that feed it, created temporary foraging areas for black stilts.