The future of the Portaferry attraction had been in doubt until the Northern Ireland Executive agreed to invest more than £900,000 in the site in 2014.
The rest of the funding was supplied by its owner, Ards and North Down Borough Council, and a new operator.
Construction will begin after Easter, to facilitate the summer re-opening.
The council has appointed the firm responsible for one of Belfast's top tourist attractions - the Crumlin Road Gaol - to run the refurbished aquarium on its behalf.
In a statement, the council said Crumlin Road Gaol Ltd (CRG) had "enjoyed outstanding success" with its existing project, as the former Belfast prison has become one of the top three visitor attractions in Northern Ireland.
Exploris opened on the shores of Strangford Lough in 1987 and became a significant tourist draw in the Ards Peninsula.
As well as being an educational visitor centre, it also houses a seal sanctuary that cares for rescued seal pups until they are strong enough to be released  back to the wild.
The aquarium was due to be taken over by a private company in 2013, but the firm pulled out of the sale after failing to reach a deal on staff pensions.
A campaign was then launched to keep Exploris open after it was threatened with closure due to its financial difficulties.
Environment Minister Mark H Durkan, whose department helped to secure the executive funding, said the planned re-opening was a "tremendous boost for the residents and businesses in Portaferry".
"I salute them and the Friends of Exploris Group for their successful campaign to keep the aquarium in their town afloat," the minister added.
"A refurbished, modern aquarium will be yet another attraction to bring tourists to our shores. Well done to Ards and North Down Borough Council for reeling this in."
The aquarium has been closed to the public since November 2014, in preparation for the refurbishment.
The Exploris aquarium in County Down is set to reopen this summer after a major £1.5m refurbishment, mostly funded by a government-backed rescue package.