At least 150 people, including many children, were on board the boat that capsized near El Hierro's harbor on Wednesday, Spanish media report.
Spanish rescue services and sea rescue responded to retrieve people from the water. One of the fatalities was found by divers.
A three-year-old boy and a five-year-old girl, who both nearly drowned, were severely injured and airlifted by ambulance helicopter to the island of Tenerife.
Spain receives tens of thousands of migrants and refugees from West Africa annually. Between January 1 and December 5, 2024, at least 10,457 people have died or gone missing during the journey, according to the aid organization Caminando Fronteras.