The effects of climate change and a dry spring has left water levels in parts of the north-east “critically low”.
Sepa has outlined increasing shortages across the region, with one part of the north-east reaching its lowest ever level.
He said: “The severity of the water scarcity picture in parts of the north of Scotland is further evidence that water scarcity will become more and more prevalent across Scotland – and is just one of the many consequences of climate change the country faces.
“We want to work with businesses to plan long-term about their water usage so that we can preserve the resource as effectively as possible.
“This will protect both Scotland’s rivers and lochs and reduce their business risks.”
Sepa’s weekly update shows Moray and huge parts of Aberdeenshire listed as having moderate scarcity.
Deerdykes, a monitoring site located around 15 miles north of Aberdeen, is the location that has recorded its lowest ever level.
The rest of the north-east and parts of the Highlands are listed as being at alert or early warning level, while most of the rest of Scotland has normal conditions.
The news will come as a surprise to many given the stormy conditions and wet weather seen over the summer but figures from Sepa show that most of the region has had lower than average rainfall during the past six months.
A water scarcity situation builds up over a long period of time and the missing rainfall would have topped up reservoirs, raised groundwater levels and provided moisture in the soils.