As of Tuesday morning, around 6,000 people had crossed the border by sea into the Spanish city since the first arrivals started early Monday. Of these, 1,500 are believed to be adolescents.
Footage showed the armed forces arriving at the beaches and arresting some of those attempting to cross.
As of noon Tuesday, some 2,700 migrants had been returned.
Spanish Prime Minister Pedro Sanchez said anyone who entered Ceuta illegally would be deported.
“We will restore order in the city and its borders,” he said.
He added that the sudden increase in migrants is a serious crisis for Spain and Europe, and that he will visit the region soon.
Spain had previously announced that troops would be deployed in the region, with border patrols starting “immediately”.
About 200 additional police officers have been dispatched to Ceuta, with 1,200 officers already in the area.
Drenched migrants, swimming or paddling in inflatable boats, still arrived on Tuesday, although in smaller numbers due to increased police and military response on the Spanish side of the border.
A spokesperson for the Espanol Authorities said one person died during the migration.
Adults were transferred to a football stadium before being sent back to Morocco, while minors were sent to an industrial building.
Ceuta, with a population of 80,000, is located across the Mediterranean from Gibraltar, and shares a land border with Morocco.
The film showed the crowds crossing the waters on Monday, with many people running or giving up their thumbs as they entered Spanish territory.
Ceuta and Melilla – which lie 150 kilometers further east – typically attract African migrants seeking to travel to Europe.
Spanish television reported that around 85 people climbed the border fence to enter Melilla.
Foreign Minister Arancha Gonzalez Laya told national radio that people who crossed the border illegally are already being returned to Morocco.
She added that Spain “will keep a cool head”.
Tensions between Spain and Morocco are on the rise following the hospitalization of Brahim Ghali.
Mr. Ghali is the leader of the Algerian-backed Polisario Front, which contests Morocco’s claim to the Western Sahara region.
Morocco was angered that Spain admitted the 71-year-old to the country – with the North African state claiming it was done under a false name and without informing them.
Reuters also reports that Mr. Ghali is being treated in a Spanish hospital.
Foreign Minister Gonzalez Laya added that she believed the influx of migrants was not a retaliatory measure for Mr Ghali’s treatment.
She said: “I cannot speak for Morocco but what they told us a few hours ago this afternoon is that it is not due to the disagreement (on Ghali).
“Spain has been very clear and detailed on the matter. It is simply a humanitarian issue. ”