While Italy and Malta's decision to turn the rescue ship away sparked worldwide condemnation, it has also shone a harsh spotlight on Europe's flawed migration policies and has reignited a bitter debate about how the bloc should handle illegal immigration.
The Aquarius rescued the migrants off Libya's coast last weekend but Italy's new populist government and Malta both refused to let it dock, accusing each other of failing to meet their humanitarian and European Union commitments.
Spanish Prime Minister Pedro Sanchez offered to take the ship in, meaning it had to travel an extra 700 nautical miles after plucking the migrants from unstable boats off the coast of Libya.
The remaining migrants arrived on an Italian coast guard ship, the Datillo, and an Italian navy vessel, the Orione. Some of the migrants were transferred from the Aquarius to the two Italian boats.
About 100 of the migrants were on board the Aquarius.More news: Distraught child migrants heard in audio published by ProPublica
The migrants, a lot of them from Africa, were welcomed by a team of more than 2,000 people, including 470 translators and 1,000 Red Cross volunteers who distributed basic items such as blankets, clothes and hygiene kits. Police officers have also been drafted in to handle their arrival.
"This sad odyssey of the people on the Aquarius is another reminder that all people, regardless of their nationality or immigration status, should have access to basic assistance and protection", Sy said in a statement.
"People were threatening to jump into the water (during) the standoff between Italy and Malta, because they were scared and said if we have to die we'd rather die at sea than in Libya".
"It is the end of a far-too-long voyage", said the head of MSF Spain, David Noguera.More news: Second place is worthless - Rivaldo admits pressure is on Neymar and Brazil
"These men women and children fled poverty and wars", she told the same news conference. Rome says only migrants rescued by Italian ships can be brought to Italian ports.
More than 1,000 migrants tried to jump a high double fence between Morocco and the Spanish enclave of Ceuta yesterday (1 January) in a violent assault that saw one officer lose an eye, local authorities said.
France has offered to take in any passengers who qualify for asylum and want to go there.
Spain's new Socialist government has taken up the cause of the migrants to demonstrate its commitment to protecting human rights.
Meanwhile, several hundred more migrants were aboard an Italian coast guard vessel off Sicily on Sunday.More news: Bavarians give Merkel two weeks to reach EU deal on migrants