Weeds pose the greatest threat to economic development and the natural resources of the Tiwi Islands. They have been a feature of the Tiwi landscape for many years and are mostly confined to communities and other disturbed land.  As with other Aboriginal-owned areas, the Tiwi Islands were selected by government for pasture and plantation forestry research trials, particularly during the 1960s and 1970s, and weeds were brought over from the mainland.  The increase in traffic from the mainland in recent years has resulted in an increased risk of the introduction of weeds and weed seed. The most common weed species on the Tiwi Islands include Mission grass (Pennisetum polystachion) and Guinea grass (Megathyrsus maximus). These African grasses out-compete native grasses and increase fuel loads, resulting in more intense fires late in Kumunupunari, the dry season. Mimosa (Mimosa pigra) and Lantana (Lantana camara), which are Weeds of National Significance, occur in two small isolated areas, and are being eradicated by the Tiwi Land Council.

Management of weeds is challenging as the Tiwi Islands are large, remote, unpopulated, and difficult to access. Weed control, as part of the Tiwi Weed Management Plan, is a key activity of the Tiwi Land Rangers and requires ongoing resourcing. 

Unlike many other areas in the Northern Territory, there is real potential to eradicate many invasive weeds from the Tiwi Islands.  Once outbreaks have been controlled, the sea barrier from the mainland combined with improved quarantine infrastructure and procedures, would make it possible to maintain a relatively weed free status.  Visitors to the Islands are asked to help the Tiwi Land Council fight weed infestations by carefully checking luggage, vehicles and freight.