Some have checks they cannot cash until it re-opens.
With end of the year bills due, farmers are looking for a solution in Washington soon.
"Everybody complains about clean water, here we are doing something to improve water ways... and it will not be getting taken care of because the government isn't there to assist with it" says farm owner Clark Riemer.
He wants to bury new irrigation lines on his Luxemburg farm, but cannot get the plans approved by the furloughed government engineer.
"If he is not there when it comes time to dig, then we will not be able to do that project this fall" Riemer says.
The project also qualifies for federal funding, but with offices closed no money is exchanging hands.
"Normally it would not be such a big deal, but the price of corn is about half of what it was last year so it would be nice to use it to pay year end expenses and stuff like that" he explains.
No new loans are being issued and local producers who already borrowed from the Farm Service Agency (FSA) cannot cash checks.
"Those are usually made out to the farmer and the FSA office. The FSA office has to sign off" explains Zen Miller, Dairy & Livestock Agent with the Outagamie County, UW Extension.
The shutdown is also affecting markets due to the lack of USDA data.
"We are establishing prices off of old data, from before the first of October" Miller says.
Farmers aren't getting daily price reports and that is leading to an uncertain economy.
"We like to keep growing the business over time but I will not be making purchases and stuff that I would have" Riemer says.