The Royal Botanic Garden in Edinburgh suffered extensive damage when a storm swept across the country on January 3, 2012.
About 600 glasshouse panes were lost, 34 trees were blown over and hundreds more shrubs and trees were damaged.
A restoration appeal raised more than £15,000 from members of the public and around 95% of the repair work has now been completed.
However, experts say the loss of many solid, well-established trees has resulted in the disappearance of crucial shelter at the gardens, making them more exposed to the elements and vulnerable to future storms.
David Knott, curator of living collections, said: "I think it's the collective gaps in the canopy that concern me, looking to the future.
"In the garden, vistas that were not evident last December quickly appeared in January.
"The concern that we have is that if you can see these new views, the wind will find its way through there.
"I'm quite pessimistic in thinking that perhaps with every wind or gale or storm force wind that we get now, that damage and the gaps will be further widened and then we'll continue to sustain damage for a good long time in the future, perhaps tens of decades."
Mr Knott added: "We reckon this was perhaps the worst storm in 30 to 40 years. It was a really peculiar weather pattern that came through Edinburgh on that morning.
"Whether that's once in 50 years or twice in five years, we don't know. But because of the gaps we have in the canopy, until we can get trees to fill that void, I think we will be at the mercy of the elements."
The gardens lost a number of significant trees during the storm, including a striking pine, a Chinese Tree of Heaven collected more than 100 years ago and a 15m (45ft) native oak.
Over the last 12 months, pain-staking work has seen around 175 new trees and more than 400 shrubs planted outside.
Another priority was to reglaze the heated glasshouses which had been left exposed to the cold. "The intensity of the wind increased from early morning to mid-morning, so we were actually able to witness the damage unfold," said Mr Knott.
"The glasshouses were particularly badly affected. We lost somewhere in the region of 600 panes. There were a number of key things we wanted to get done quite quickly. We reglazed the glasshouses in a record period, somewhere in the region of seven to eight days.
"In some of the ones that were particularly badly affected, we had to remove shards and tiny pieces of glass. That work is still ongoing. Outside, we tried to make sure the access paths were open, but that took us a bit longer.
"We've looked very carefully at what we've lost and tried to replant. I would say we're maybe 95% there with all the work, but it's been a long process and it's a testimony to the hard work of the staff."
The restoration appeal remains open and the gardens continue to welcome donations to help with the work.
Anyone who wishes to donate should contact 0131 552 7171 or visit www.rbge.org.uk/home