After a four-day crossing of the Mediterranean, the 60 migrants -- 50 men, five women and five minors including three who were unaccompanied, according to the NGO -- were due to be examined by Red Cross workers.
They will then be transferred to shelters.
They "are doing well given the circumstances, there was no serious medical emergency and they're happy because we told them the government wanted them to come here," said Anabel Montes, the NGO's project manager.
The Open Arms ship arrived in Spain over two weeks after the Aquarius, a French NGO rescue vessel carrying 630 migrants, was given authorisation to dock in the eastern port of Valencia.
It had been refused access by Italy and Malta in what caused an international outcry.
Malta then let another charity rescue boat, Lifeline, dock with 23 migrants aboard.
- ‘It’s been a long time since I was hugged like this': Aquarius girl, 12, to rescuer
- Spain and Greece accords help Merkel ease migrant row
EU leaders have accused charities of playing into the hands of people smugglers with their missions rescuing migrants off the coast of Libya.
On Wednesday, the Sea-Watch charity said Malta has blocked its reconnaissance plane "Moonbird" from taking off, after impounding its Sea-Watch 3 vessel on Monday.
"It's obviously in order to prevent rescues at sea," Sea-Watch spokesman Ruben Neugebauer told AFP.
The plane, which is operated in conjunction with a Swiss pilot relief group as well as backed by Germany's Protestant churches, is used to help spot migrants in distress at sea.
"About 1000 would have drowned for sure, if our #Moonbird would not have found their sinking boats at the last second," said Sea-Watch on Twitter.
Faced with growing tensions in the EU over the issue, member states struck a deal on Friday to stem the arrival of migrants.
The accord includes the setting up of secure centres for migrants in the bloc, "disembarkation platforms" outside the bloc and sharing out refugees among member states.
On Wednesday, Activists in Barcelona climbed the statue of 15th-century explorer Christopher Columbus and hung up a giant orange life-vest to highlight the loss of migrant and refugee’s lives in the Mediterranean Sea.