The Aquarius picked up 141 people on Friday in two separate operations, SOS Mediterranee and Doctors Without Borders said on Twitter.
The Aquarius "remains in the search and rescue zone, and on the lookout for any other craft in distress".
In one of Friday's operations the Aquarius took on board 116 people, including 67 unaccompanied minors, mostly from Somalia and Eritrea.
Their wooden boat was overloaded and carried neither water nor food when it was spotted some 24 nautical miles off the Libyan coast, north of Abu Kammash.
Earlier the same day, the vessel had already rescued 25 migrants who were travelling in a small wooden craft, also off the Libyan coast, north of Zouara.
This marks the return of the vessel after a diplomatic spat that began in the night of June 9-10 when the Aquarius, having picked up 630 stranded migrants including children and pregnant women, was refused access to docks in Malta and then Italy.
Italy's far-right Interior Minister Matteo Salvini later threatened to turn away any migrant rescue boats, sparking a fresh row among the EU's 28 members over how to handle the influx of people fleeing war and poverty.
After the ship was stranded at sea for days, the new Socialist Spanish government offered to let it land at Valencia, where its passengers disembarked on June 17.
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