The Millport marine base, on the Isle of Cumbrae in the Firth of Clyde, is expected to reopen in February after being temporarily shut last year when previous owners the University of London withdrew support.
The science station, which is now run by the Field Studies Council and Glasgow University, has been given £500,000 from the Regeneration Capital Grant Fund, which is run jointly and funded by the Government and COSLA, and £500,000 from the Scottish Funding Council.
The funding follows a series of last-ditch talks between Cabinet Secretary for Education and Lifelong Learning Michael Russell and parties hoping to keep the base open.
Mr Russell said: "Over the past few months we have worked very hard with partners including North Ayrshire Council, COSLA, the University of Glasgow and the Field Studies Council to find a sustainable way to rescue the Millport marine base and safeguard its contribution to the local economy.
"Those efforts are paying off and I am delighted that the Scottish Government has been able to provide a total of £1m to help secure the future of the base.
"The station is expected to re-open, under new owners, in February and this is a significant success for all those who have played a role in developing plans."
Robert Lucas, chief executive officer of the Field Studies Council, added: "The Field Studies Council welcomes this critical funding for the Marine Station at Millport and is delighted to have the opportunity to develop a new and sustainable future for the centre building on its international reputation for marine science field teaching. "
Councillor Willie Gibson, Leader of North Ayrshire Council, said:
"I am delighted to see so many organisations pledging real support to ensure the Millport marine base has a bright future."