The Aquarius is operated by the aid groups SOS Mediterranee and Doctors Without Borders to save people in distress in the Central Mediterranean, the most deadly migration route in the world.
Malta refused and Spain stepped in and offered to grant them entry some 930 miles away.
The 930-mile journey across the Mediterranean from Sicily to Valencia took almost a week.
The migrants' arrival in Spain ended a weeklong odyssey after Italy and Malta refused to let the rescue ship dock.
As many as 986 people were rescued at sea and four died in the past 48 hours as they made their way from North Africa to the Straits of Gibraltar and Spain's western Mediterranean coast, the Spanish maritime rescue service said on Saturday.
"I have mixed feelings", Noguera told The Associated Press as the first boat arrived in Valencia.
The refusal by Italy and Malta to allow the Aquarius to enter their ports has created a row between European Union members over how to handle immigration.
The migrants were met by emergency workers, health officials, Red Cross volunteers and psychologists at the city's marina. Each were assigned to a translator and authorities worked to determine their identities before they were sent to welcome centers.
The first person through the process was a 29-year-old man from South Sudan.
Incoming Chelsea boss Maurizio Sarri 'wants to sign Dries Mertens'
And Chelsea aren't the only club with an interest in the forward. " When a person like this comes to a new club, he needs time ".
The Democratic Party's president, Matteo Orfini, responded to Salvini by posting a sharp retort to his proposal for a Roma census by asking whether it would be more appropriate to count the number of racists and fascists in the country instead of focusing on migrants and non-Italians. I tell them I don't want to circumcise my children.
France has said it will examine asylum requests from Aquarius migrants who want to come over from Spain on a "case-by-case basis", government spokesman Benjamin Griveaux said Sunday, although he did not know how many might make the requests.
Physical exams did not reveal any serious health problems, but many passengers showed signs of exposure to high temperatures.
Shouts and singing erupted on the ship as the migrants on board saw Valencia on the horizon, Spanish journalist Gabriela Sanchez tweeted from another boat travelling alongside it. "But now we must collectively reflect on the reasons for people fleeing across the Mediterranean".
"So people are in a bad state..., and they are really relieved to come on safe land at the moment".
Migrants arrived here with nothing, Corral said.
Jose Luis Abalos says "Spain will act with sensitivity and at the same time within the law, and with a message to Europe that it doesn't have an immigration policy up to the challenge at hand".
"Without clothes, or memories of the lives they left behind, however, they are still caring", he said.
The Aquarius picked up the 630 migrants off the Libyan coast last week.
When the Aquarius was coming close to one of the small wrecked boats which carried dozens of refugees, a child, without clothes and shaking, was climbing overboard desperately after falling into water, Corral said, "I was deeply shocked by it".