Negotiations with unions had been stalled for nine months; the dispute has snarled recent traffic at the facilities, which handle $1 trillion in cargo each year.
Scientists believe the project, which is reportedly underway already, could destroy a million acres of rainforest and contaminate Central America's largest source of drinking water.
Jacksonville, Fla., is racing to find funds to deepen its port. If it can't accommodate newer, bigger cargo ships from Asia, the city says, it will lose out to Savannah, Ga., and Charleston, S.C.