Then there are the steeply discounted business loans, which have a measurable impact on what farmers decide to plant. In many cases, to be eligible for these subsidies one year, a farmer has to have previously planted the crop — a basic component of the bill’s architecture that gives farmers an incentive to maintain “base” levels of acreage. In an analysis, the Congressional Budget Office found that the subsidies don’t just maintain the status quo, they also foster more planting, and more water use. The USDA’s marketing loans alone, for example, led to a 10 percent increase in the amount of cotton farmers planted — compared to 2.5 percent increase in the amount of wheat, and a 1.5 percent increase in the amount of soybeans produced — in part because the subsidies not only make cotton a safer bet, they also make it more competitive against alternative crops. Banks lend cotton growers money they wouldn’t lend for other crops, largely because they know the government will stand behind them.

All told, Wuertz estimates that nearly one-fifth of his income is derived from Farm Bill aid, and cotton has almost always been his largest and most important crop. According to USDA statistics compiled by the Environmental Working Group, the Wuertz family — including his brother’s and father’s farms — has received more than $5.3 million in farm bill subsidies since 1995, a portion of which may have been targeted for efficient irrigation equipment, Wuertz said.

The Farm Bill has been used in the past to steer environmental policy. It provides for withholding money, for example, from farms that would contribute to soil erosion or the destruction of wetlands. In North Dakota, where farmers were tearing out grasslands to plant corn for ethanol production, the law contains “sodbuster” provisions withholding insurance benefits from those who rip up lands the government wants to conserve.

The Farm Bill contains $56 billion for conservation, funding an effort to encourage farmers to reduce their water consumption by using more-modern equipment as well as measures meant to conserve land. Another section of the bill is aimed at saving energy. But the law’s farming incentives run counter to its far more modest water conservation initiatives.

“There is a real disconnect between that and what the commodity and crop insurance program are promoting, and that’s a basic conflict,” said Ferd Hoefner, the policy director at National Sustainable Agriculture Coalition, based in Washington, D.C.

The Farm Bill’s authors have sometimes factored in environmental concerns in specific places and tailored incentives to affect them, Hoefner said. But when it comes to cotton, the bill does not consider the related water use, and it does not distinguish between the places where it is grown. Instead, the money corresponds roughly to the amount of cotton harvested; Arizona, which ranks in the middle in terms of its cotton production, also ranks 10th among the 17 states that receive cotton aid. California, which ranked third for overall cotton production in 2013, also ranks third in subsidies over the last 20 years according to data collected by the Environmental Working Group. It’s in those places that the incentives created by the subsidies are most in conflict with the government’s aid to conserve water.

“Trying to get USDA to break down the silos is difficult,” Hoefner noted.

The Congressional Budget Office attacked this disconnect in 2006, urging the USDA to stop supporting agricultural products that act to “impede the transfer of water resources to higher value uses,” and “encourage the use of water.” Analysts advised the USDA to enhance its conservation programs, align its subsidies with those conservation efforts, and stop paying for infrastructure that makes water artificially cheap.