A tropical cyclone is expected to develop on Saturday in the Gulf of Carpentaria, with the Bureau of Meteorology (BOM) issuing a cyclone watch for coastal communities from Groote Eylandt down to the Northern Territory-Queensland border.

The BOM is forecasting the system to move slowly south towards the south-western Gulf of Carpentaria coast, before most likely quickly weakening early next week as it crosses the coast.

"This [watch] is for a developing low pressure system that's currently located near the Gove Peninsula," BOM forecaster Rebecca Patrick said.

"It has moved quite quickly overnight across the northern coast of the Top End and is expected to move into the Gulf of Carpentaria over the next 24 hours."

The tropical low is predicted to bring strong winds and heavy rain to the region, particularly to the south-western Gulf coast.

"We could see some gale-force winds developing over Groote Eylandt as early as [Saturday] morning, with gales also potentially developing over other Gulf of Carpentaria coastal areas later on Saturday or Sunday," Ms Patrick said.

Damaging wind gusts of 110 kilometres per hour could develop over Groote Eylandt, according to the BOM's website.

"Gales with damaging wind gusts of 100 kilometres per hour may extend further to the Northern Territory coast between Alyangula to the Northern Territory/Queensland border, including Borroloola, from as early as Saturday evening, though more likely during Sunday," the BOM said.

"Destructive winds gusts are also possible for the south-western Gulf of Carpentaria coast from late Sunday depending on how quickly the system moves south."

The BOM said heavy rainfall was already occurring over north-eastern parts of the Top End and was expected to increase into the weekend.

"With those heavy rain conditions, we are expecting those over the Arnhem district to continue and we could see some very heavy rainfall, particularly in those coastal locations and also extending further south as we go into Sunday and early next week," Ms Patrick said.

"That system [is] expected to move southwards through potentially the Carpentaria district or possibly anywhere along the southern Gulf of Carpentaria coast."

Top End on flood watch

Parts of the Top End have experienced heavy rainfall over the past week.

The BOM said rainfall totals of up to 147 millimetres had been recorded across a broad flood watch area in the past 24 hours, following several days of heavy falls.

Showers and thunderstorms with isolated heavy falls are forecast over the next few days, the BOM said, with widespread daily totals of 50 to100 millimetres and isolated totals possibly up to 200 millimetres expected.

There are currently the following flood warnings in place in the Northern Territory:

• A flood warning for the Victoria River.
• A moderate flood warning for the Daly River.
• A minor flood warning for the Katherine River.
• A flood watch for the Top End.

Pigeon Hole again hit by flooding

The community of Pigeon Hole was once again flooded this week due to the widespread rains, with residents having to relocate to the community's flood shelter.

The community also known as Nitjpurru, which is located 700 kilometres south of Darwin and built on a flood plain, was evacuated following flooding in 2023 and also earlier this year.

Anne Pollock, a local teacher who grew up in Pigeon Hole, said the community was on edge.

"Over the weekend we thought we should start moving people to higher ground, and we took up camping gear and camp ovens from our kitchens," she said.

"On Monday I was collecting people and taking people to the evacuation centre.

"Some people were worried about their homes being flooded … it's always a worry [when] our homes get flooded."

An NT government spokesperson said an emergency declaration had been signed for the community on Wednesday, which "allows the government to take necessary steps to ensure community safety".