There are many reasons children end up staying. Some see their cases linger in backlogged courts and administrative proceedings. Some win the legal right to remain in the U.S. And some ignore orders to appear in court.

Children who enter the U.S. illegally often are trying to reunite with family members or escaping gang violence and poverty. The U.S. has been overwhelmed finding shelters for them, and Mr. Obama has repeatedly said that they won’t be allowed to stay. But the reality on the ground—that so few are returned to their home countries—will continue to encourage more to make the journey north, said Doris Meissner, director of the Immigration Policy Program at the nonpartisan Migration Policy Institute.

“They’re here, and they’re staying, and whatever else might happen to them is at least a year or more away,” said Ms. Meissner, a former Immigration and Naturalization Service commissioner. “Until people’s experience changes, more are going to continue to come, because they’re achieving what they need: safety and reunification with their families.”