Farmers in the Holland Marsh are racing to pump flood water's out of their fields after Thursday night's downpour.

Farmer Jason Verkiaik and his team are busy digging trenches to speed up the drainage at their farm.

"Yesterday evening I was in here doing work with the tractor. Last night three inches of rain and it's flooded again," he says. "About 40 per cent of our fields do have surface water. All the stops are out to get the water away as quick as possible cause that's how we can save the crop."

About 75 millimetres of rain soaked the marsh on Thursday night. Dozens of acres of onions and carrots are covered in ankle deep water.

"The crop itself is very small. If it was bigger it could absorb it, but this is just too much," says farmer Tony Morro.

Farmers say they will still produce a crop, but it's too soon to know how much damage all this rain has done.

“The window for re-seeding onions is long gone. If there is any re-seeding carrots that can be done, but you have to give it time to go down."

There is an underground drainage system that flows into the river, but it was just too much rain at once for it to handle it.

"Many of the tiling systems that are in the fields are actually lower than the river level. It can actually back flow into the fields," says Frank Jonkman, drainage superintendent.

Another factor, two pumps failed last night at a station believed to be caused by a lightning strike. That's now been fixed. 

"We're pumping as aggressively as we can. We actually caught the crest right now, but again we're going to be very aware of weather events coming in."

With more rain in the forecast, more pumps are being installed to drain the fields. They will continue running non-stop.