Wellington Shire residents are on high alert as flood waters pose a renewed threat for a second time in less than two months.

Flood warnings have been in place for the Macalister River, Thomson River, Mitchell River, Tambo River, Gippsland Lakes and Avon River since Tuesday, as a low-pressure trough is causing widespread rainfall across the state.

Emergency Management Victoria issued an initial flood watch for the Macalister River, Thomson River, Mitchell River, Tambo River, Gippsland Lakes and Avon River at 1.30pm on Tuesday.

The message forewarned of widespread rain and showers over the state, with possible heavy falls in the east and south Gippsland on Wednesday and Thursday.

“Catchments are relatively dry. Widespread rainfall totals of 50 to 100 millimetres are forecast across the flood watch area during Wednesday,” the emergency warning read.

“Further rainfall totals of 40 to 80 millimetres are forecast on Thursday with isolated higher totals possible.

“River level rises are expected, and minor flooding is possible for the catchments listed from Wednesday. Potential for moderate to major flooding with higher possible rainfall totals.”

Rainfall developed overnight with no ease to the downpour come Wednesday morning.

Shortly before 12.30pm, the Bureau of Meteorology issued a severe weather warning for Gippsland, cautioning heavy rainfall and possible damaging winds.

“The low-pressure system will move into the Tasman Sea just off that southern New South Wales coast on Thursday, and in response, it will be dragging that moisture down from the tropics, also ingesting that moisture that’s coming off the Tasman Sea, which has got high sea surface temperatures at the moment and funnelling it into Gippsland in particular,” senior meteorologist Kevin Parkyn said.

“We’re already starting to see rain rates increase through parts of southern Victoria, in fact, just in the last four hours, we’ve seen this very moist southeasterly flow result in 50 millimetres into parts of the Otways, and that’s just since 9am.

“We’ve seen falls locally as much as 50 to 60 millimetres in the Strezleki Ranges and through the Gippsland Foothills, but it’s just starting.”

The Bureau of Meteorology forecasted rainfall to intensify into the night and continue into Thursday, with Gippsland expected to receive in excess of 100 millimetres over the next 24 to 36 hours.

“What that means in terms of the catchments, of course, a lot of this rain will be good news but also, unfortunately, where we do see this intense rainfall, particularly through the Gippsland catchments, it will result in flooding,” Mr Parkyn said.

“We think a lot of the rivers will end up with minor to moderate flooding, but depending on the rainfall we see on Thursday, there’s certainly the potential for some of our river systems to trigger into major (flooding), so the Bureau of Meteorology has issued a flood watch for riverine flooding particularly through those Gippsland rivers but also for the Barwon, the Maribyrnong and the Werribee river systems as well.”

In addition to the heavy rainfall sweeping the state, emergency warnings have also been issued for strong southeasterly winds.

“Across the state today, we’ve seen southeasterly wind gusts peaking in the 70 to 90 kilometre per hour range,” Mr Parkyn said.

“It is unusual to see strong wind gusts from that direction and with the rain as well; it’s actually resulting in a fair bit of damage to vegetation and trees on roads.

“The Bureau of Meteorology has issued a severe weather warning that captures the depth of the risk of damaging winds on top of the risk of heavy rain leading to flash flooding.

“It’s very much a ‘watch this space be prepared’ over the next 24 to 48 hours for the heavy rain leading to flash flooding, but also for the riverine flood risk as well.”

The downpour continued throughout the afternoon, with Mount Moornapa receiving more than 35 millimetres of rainfall in the nine hours to Wednesday, 6pm.

East Sale Airport recorded a little more than 11 millimetres between 9am and 6pm on Wednesday, while Yarram Airport recorded 15.4 millimetres.

Emergency Management Victoria issued a moderate flood warning for the Thomson River to Cowwarr Weir at 7.10pm.

“Minor flooding is occurring along the Thomson River to Cowwarr Weir,” the emergency warning read.

“The Thomson River upstream of Cowwarr Weir is currently at 3.96 metres and rising above the minor flood level (3.70m).

“The Thomson River U/S Cowwarr Weir may reach the moderate flood level (4.50 m) overnight Wednesday into Thursday.”

At the same time, an initial minor flood warning was issued for the Thomson River, Cowwar Weir to Wandocka.

“Minor flood occurring at upstream Cowwarr Weir,” the emergency warning read.

“Forty-eight-hour rainfall totals of up to 90 millimetres have been recorded to 6pm Wednesday across the Thomson River catchment, resulting in strong river level rises.

“The Thomson River at Wandocka is likely to exceed the minor flood level from Thursday morning.”

Just before midnight on Thursday, Emergency Management Victoria issued a minor flood warning for the Macalister River downstream of Lake Glenmaggie.

“The Macalister River downstream of Lake Glenmaggie is currently at 1.57 metres and steady,” the warning read.

“The Macalister River downstream of Lake Glenmaggie is expected to exceed the minor flood level (2.60m or 7,500 ML/d) Thursday morning.

“In the past 24 hours to midnight Thursday, up to 90 millimetres of rainfall has been recorded across the Macalister River catchment, causing river level rises.

“Further rainfall is forecast for the next few days, with a further 40 to 60 millimetres possible.”

As of 12.15am on Thursday, there was a total of 17 active emergency warnings within a 60-kilometre radius of Sale.

Among the emergency warnings were a moderate flood warning for Thomson River to Cowarr Weir, a minor flood warning for the Macalister River downstream of Lake Glenmaggie, a flood watch for the Macalister River upstream of Lake Glenmaggie, and a minor flood warning for Thomson River Cowwar Weir to Wandocka.