Researchers used flow projections from across the country to model which regions and industries could be affected by droughts between 2020 and 2049.
They considered the impact of climate change on abstraction – water that is licensed to be removed from locations such as rivers and lochs – and found some areas could see droughts becoming much more frequent.
Professor Lindsay Beevers, from Heriot-Watt University, said: “We wanted to identify existing and emerging drought hotspots in Scotland where more frequent, longer droughts are likely.
“Our analysis shows that droughts could become two to three times more frequent across much of Scotland.
“Abstraction is vital for our economy. Knowing which areas could face water scarcity means that we can plan and adapt to protect our economy and the environment.
“We can learn a lot from the south of England, where they have come up with some really interesting ways to balance supply, demand and storage.”
Tiffany Lau, from SEPA, said: “SEPA is clear that by taking the right steps now, we can reduce the impact of water scarcity in the future.
“By working with the water sector we can ensure the reliable supply of Scotland’s high-quality water resource is maintained.
“Increasingly Scottish businesses are aware of the need to plan for the future by adopting and developing their own water-saving innovations and SEPA will help them do this.”