Read MoreCalifornia farmers shore up for El Nino
Plumped waterways are impacting some barge traffic in and around the Midwest down to the Gulf Coast, and involves such channels as the Mississippi River, Maltsbarger said. Crops and food impacted so far include corn, soybeans and fertilizer, which is used in nearly every pocket of food production.
"For now it's short-term impact," said Maltsbarger. Other floods in recent years have led to widespread river closures that impacted, for example, the movement of grains, according to IHS research.
"If we move into the spring and we get these increased rains, it will have a much bigger impact," Maltsbarger said. "There's prime farmland along the rivers that could get flooded."
The fact that barges are even used for shipment of agricultural goods may come as a surprise. But hauling goods on waterways — everything from coal to grains — predates America's railroads, and can cost a fraction compared to shipping goods by rail.
Specifically for the delivery of agricultural products, barges today are the equivalent of massive, steel bathtubs and are the second-biggest transportation mode behind railroads, said Charles Clowdis, managing director of transportation at IHS. "Barges are a very dependable type of transportation," he said.
Taking into account El Nino's impact on multiple sectors, including agriculture, the overall net effect of El Nino typically is small but positive. The economic benefits of the 1997–98 El Nino event — the most severe to date — were about 0.2 to 0.5 percent of GDP. IHS expects impacts on the same order of magnitude during the 2015–16 El Nino.
The current El Nino is forecast to affect temperature and precipitation patterns across the U.S. in the coming months. There's an "increased likelihood of above-median precipitation across the southern tier of the United States, and below-median precipitation over the northern tier of the United States," according to the National Weather Service.