[5][6] It has been chartered and operated since February 2016 by the NGOs SOS Méditerranée and Médecins Sans Frontières (MSF or Doctors without borders) as a rescue vessel for migrants and refugees making the Mediterranean crossing in makeshift craft from Libya to Italy as part of the European migrant crisis.

Here it operated until the end of 2015 as a survey vessel for renewable energy, oil & gas industry, and other offshore projects.

[4] On 16 August 2018, the ship was inspected by the Port state control (Pais MoU) at Valletta (Malta) and five deficiencies were found related to the crew certificates, oil record book and blocked routes of escape.

A Ghanaian boy was born on board who was subsequently named Alex in honor of the Russian captain of the Aquarius, Alexander Moroz.

[13][14][15] In June 2018 the ship, carrying 629 migrants from Sudan and Bangladesh saved from the sea, was denied entry to Italy by its new Interior Minister Matteo Salvini and to Malta as well.

[27] The same day the Aquarius asked Italy and Malta permission to disembark the eleven migrants and both countries refused.

On 6 August 2018 the Gibraltar Maritime Administration issued a "notice of removal" for the Aquarius, because she was registered as a survey vessel, but used as a rescue ship.

[33] However, on 22 September 2018 the maritime authority of Panama announced that it had initiated procedures to remove the Aquarius from its registry, quoting violations of international law with respect to migrants, rescue at sea and refusing to carry the migrants back to the area where they originated (UNCLOS, SOLAS and SAR convention).

The Government of Panama initiated the process based on information received from Italy that the Aquarius had not followed international regulations and legal proceedings concerning the transport of migrants.

After the ship returned to Marseille in early October 2018 the owner issued a statement about negotiating to obtain a new flag from Switzerland, Luxembourg or Venezuela.