Costa Rica had asked the court to bar Nicaraguan troops from the disputed region and order it to halt dredging and tree felling in the region where the San Juan empties into the Atlantic Ocean.
Instead, the court on Tuesday ordered both Costa Rican and Nicaraguan forces out, and told both countries to "refrain from any actions which might aggravate or extend the dispute. Costa Rica went to the court last year claiming Nicaragua illegally sent troops and engineers into Costa Rican territory to dredge part of the river.
The area has been a source of tension between the two nations for more than a century. Costa Rica has no army but allegedly mobilized police forces to the border. When it went to court last year, the Costa Rican government also complained that the border depicted by Google maps was wrong and favored Nicaragua.
Google later corrected its version of the border, blaming faulty data from the U.S. State Department that had led to ceding as much as 1.7 miles of territory to Nicaragua.
The Nicaraguan military officer in charge of the dredging operation denied reports that he had used an erroneous Google map in planning the work, according to local media.
In Managua, the leftist government of President Daniel Ortega, a former Sandinista guerrilla leader, denied any incursion into Costa Rican territory and said its troops were on the ground to fight drug trafficking.
Nicaragua claims it is operating in its territory based on previous treaties and a 2009 decision by The Hague-based International Court of Justice.