VICTORIA is labouring under its worst floods in 15 years but many farmers are rejoicing.

Torrential rain dumped 50-200mm in the North East and western Victoria over the weekend, flooding small communities.

Wangaratta, Myrtleford, Benalla, Euroa, Creswick, Avoca and Glenorchy were among the worst affected.

Several towns - including Horsham, Shepparton and Wangaratta - remain on high flood alert.

The washout has seen:

Milk dumped on some farms as tankers can't access dairies.

Saleyard numbers dropping or sales cancelled as stock cannot be brought to market.

Crops destroyed by water.

The Victorian Farmers Federation call for the north-south pipeline to be shut down.

Early warnings have kept stock deaths to a minimum as producers took the chance to move animals to higher ground. How badly crops and pastures are affected will become clearer as flood waters recede.

The Wimmera River, in the state's west, burst its banks on Saturday night at Glenorchy and flood waters have ravaged nearby towns.

Lubeck farmer Ian Taylor said at least half of his 2800ha property was under water and some of his neighbours had lost stock to the floods.

"It's probably one of the highest floods I've ever had at my place," Mr Taylor said.

"The neighbour has lost quite a few sheep this morning ... it'd be hundreds that've been lost but we don't really know (how many) because we can't get them in the yards and count them but we've seen them floating down the river.

"There's a lot of concern. A lot of people haven't seen water like this."

Murray Goulburn Kiewa field officer Murray Wisewould said a few dairies had been flooded but "most dairy farmers were OK".

Mr Wisewould said early warning of impending floods had allowed farmers to prepare, and while they were inconvenienced, they were coping.

"As long as there hasn't been too much damage to their pastures, and infrastructure, they are pretty happy," he said.

"But while it is inconvenient now, they know the dams are full and the soil is wet and when you've got water, you've got something."

In some areas, crop paddocks which last year were a sea of dust and a week ago a luscious shade of green, are now brimming with water.

Despite concern in some of the hardest-hit areas there is a flipside.

Colin Coates, of Traynors Lagoon, west of St Arnaud, said it was amazing how quickly farmers' fortunes could turn around.

"Dams that haven't been full for 15 years are now full in two days," Mr Coates said.

Elders Ararat agronomist Michael Joss said there were "mixed emotions" among farmers.

"I think blokes are very pleased to see everything pretty well full if not filling, and as far as their stock water on farm goes it's looking very handy," Mr Joss said.

"So it is disappointing to see the crops struggling but I think all in all there's a part of all of them that's having a quiet cheer."

The Bureau of Meteorology was not prepared to say the drought is over, and said it never uses the word "drought" but "deficiencies of rainfall".

Whatever the terminology, the bureau said the weekend's rain meant there were "no recent rainfall deficiencies left".

The bureau's climate meteorologist for Victoria, Harvey Stern, said the last wet year for Victoria was 1996.

"There would be some pre-teen children who would never have seen anything like this," Dr Stern said.

"Prior to the (dry) 1990s, the first winter rains used to produce hardly any rise in the rivers but by early spring, a 25mm fall would cause a flood because the catchments would be wet from winter rains.

"We are in that kind of situation now."

Yesterday VFF president Andrew Broad called for the pumps on the north-south pipeline to be switched off.

Mr Broad said it was appropriate to keep the pipeline running until the floodwaters had eased, but should then be "turned off for a number of years."

Meanwhile, water from the Avoca River at Charlton threatened shops in the main street of the town with residents busy sandbagging the main street.

However, it's not wet everywhere.

Gippsland farmers missed out on the big rain, with most centres recording single digit figures, despite moderate flooding downstream of Lake Glenmaggie.