Call it the case of the missing nitrogen.

For decades, scientists have wondered what happens to the nitrogen that farmers apply to fields. On the farm, levels of the nutrient are high. But downstream, they’re lower — sometimes only half as much. In an attempt to figure out where it went, scientists have undertaken “mass balance studies” to solve the mystery.

Does the nitrogen dissipate into the air as a harmless gas? Does it convert to nitrous oxide, a potent greenhouse gas, and pollute the air? Does it stay in the soil — as the other plant nutrient, phosphorus, does— and eventually ooze into streams over time?

Two recent studies — one focused on the Mississippi River and one on the Chesapeake Bay — suggest at least partial answers.

Nandita Basu, an assistant professor at the University of Waterloo in Canada, and doctoral student Kim Van Meter looked at more than 2,000 soil samples throughout the Mississippi basin and found an accumulation of nitrogen in the soils. In the March issue of Environmental Research Letters, they reported finding that the nitrogen often was not in the first layer of soil, but 10 to 39 inches below the surface. There, it converts to nitrate, an inorganic compound that is the most common drinking water pollutant in the United States.

At high enough levels, nitrate in drinking water can cause “blue baby syndrome” in infants, a potentially fatal condition. Some studies also have suggested consuming water with extremely high nitrate concentrations over time could cause cancer.

It is a significant issue in Iowa, especially in the Des Moines and Raccoon River basins, where utilities have to spend millions of dollars to denitrify the water so it is safe to drink.

The Des Moines Water Works is suing three upstream rural counties for failing to protect drinking water.

Closer to home, Tom Fisher, an ecologist with the University of Maryland Center for Environmental Science, began his own investigations into the missing nitrogen with graduate student John R. Gardner and colleagues Thomas Jordan, a senior scientist at the Smithsonian Environmental Research Center, and Karen L. Knee, an assistant professor at American University. The group found that 74 percent of the nutrient applied to the crops was leaving the fields in the Choptank and Nanticoke river watersheds where the team conducted its research. But most of it never got into streams because it was transformed through natural biological processes into harmless nitrogen gas and released into the air.

But a small share — roughly 1 percent depending on temperature — was released into the atmosphere as nitrous oxide, a greenhouse gas that is 300 times more potent than carbon dioxide. Most of that was produced in streams, with about 12 percent from groundwater. Their paper was published late last year in the journal Biogeochemistry.

Though the relative amounts of nitrous oxide released are small, they are potentially important because of climate change and efforts to mitigate it.

Fisher said he’d like to repeat the work in different watersheds under different conditions to see if there’s a way to manipulate that chemical transformation so that the nitrogen remains in an inert harmless form instead of converting into a greenhouse gas.

Donald F. Boesch, president of the UM environmental science center, said Fisher’s research begins to solve the nitrogen mystery. The work might one day lead to changes in how much nitrogen farmers apply to gird against climate change and not just runoff pollution.

“We know the [stream] is a sink for nitrogen, and generally, we think this is a positive. We close the gap, close the budget,” Boesch said. “But the story doesn’t end there, because nitrous oxide is a very potent greenhouse gas, and its primary source is from agriculture systems.”

(An earlier version of this story misidentified Thomas Jordan and Karen Knee. The Bay Journal regrets the error.)