Around two-thirds of the roughly 8,000 migrants who made it to the enclave have been expelled, the interior ministry in Madrid said.
Many who were sent back said they were determined to head for Ceuta again and, as dense afternoon fog descended, hundreds of young men made a fresh attempt to approach the roughly six-metre-high metal border fence before being repelled by Moroccan police.
Others entered the water and began swimming towards Ceuta's beach a few hundred metres away.
"All my body hurts. I can't walk. I walked for three days before I reached here...The people take me, they beat me," Senegalese migrant, Mohamed, told Reuters.