Mitchell's water monitors (Varanus mitchelli) are a small to medium-sized (<1 m TL) Australian varanid lizard endemic to northern Western Australia and the Northern Territory, extending just into north-western Queensland. They are a semi-aquatic, semi-arboreal monitor, typically thought of as being associated with freshwater riparian habitats. Following the arrival of cane toads (Rhinella marina) across their distribution, V. mitchelli were observed to have suffered precipitous population declines and local extinctions due to lethal toxic ingestion of toads. Here, we present observations of V. mitchelli from previously unreported saline and brackish habitats, as well as information on the cryptic behaviour and seasonal activity of this threatened species in Darwin, Northern Territory. Currently, because V. mitchelli are undocumented in mangrove and littoral habitats, ecological consultants in northern Australia are considering such habitats unsuitable for this threatened varanid and are not recommending targeted surveys for this species in these habitats. We argue that the niche occupied by V. mitchelli is broader than currently recognised and they should be considered as potentially occurring in most mangrove habitats across their known range. We also suggest species-appropriate survey techniques to improve detection of this very cryptic threatened species. Concerningly, despite recently being recognised as Critically Endangered by the International Union for Conservation of Nature (IUCN), V. mitchelli are currently not recognised as threatened by the federal Environment Protection and Biodiversity Conservation (EPBC) Act 1999.