Great-grandfather Peter Congdon, 67, from Truro, Cornwall, scooped the money in a rollover in May.
The Merlin MS Centre said Mr Congdon's wife Rosemary had multiple sclerosis and his family wanted there to be a "lasting legacy" to her.
The charity said the exact donation was yet to be finalised but it would be a "substantial amount".
Loraine Long, the centre manager, said: "Peter and his family were very keen that they could help provide an additional service for people with multiple sclerosis and other neurological conditions.
"A hydrotherapy pool is a much-needed facility and by locating it alongside our centre, subject of course to planning approval, this will provide a wonderful natural therapy for people living with a range of conditions and to the wider Cornish community."
The widower, who has three children, 10 grandchildren and one great grandchild, has previously raised thousands of pounds for community groups.
In the run-up to buying the successful ticket on 27 May, Mr Congdon had won three days in a row on the National Lottery Scratchcards.
Ms Long said: "Everyone here is so delighted for Peter's incredible pledge.
"We would like to say a truly heart-felt thank you to them. This is our own lottery win."
The charity, based in the Cornish hamlet of Hewas Water, supports those living with the incurable condition.
A £13.5m lottery winner will fund a new building for people with multiple sclerosis, a charity has confirmed.