The agency has warned that conditions are unlikely to improve in the next week.
Despite some rainfall in recent days, many areas have continued to get drier throughout June and into July, and very little rainfall is forecast across Scotland for the week ahead.
Areas around the River Irvine and River Ayr in Ayrshire are also now at Early Warning stage, again due to low river levels. The majority of the east remains in Alert.
Businesses abstracting water in Moderate Scarcity areas are advised to only do so when absolutely necessary, stagger their operations, reduce volumes and durations or suspend abstractions altogether. SEPA can also offer support on switching supplies, such as using groundwater instead of river water.
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Abstractors in Alert areas should plan ahead as conditions are expected to worsen before improving. They should work with neighbouring water users to schedule abstractions where possible.
In Early Warning areas, the advice is for businesses to consider their upcoming water requirements, how to use water more efficiently and to check equipment for any leaks.
Water Resources Specialist at SEPA, Michael Wann, said: "Water is a resource that underpins key industries across Scotland - from food and drink production, to farming and golf course management.
"All licensed abstractors must have a plan to deal with the range of conditions they experience throughout the year, including the current deteriorating water scarcity situation.
"Water is shared and finite, and we all need to work together to manage it as efficiently as possible. We want to work with businesses to plan long-term for their usage so that we can preserve the resource as effectively as possible."
It comes after SEPA warned in March about the growing threat of water scarcity this year as a result of a particularly dry winter. It is also expected water scarcity will become a more frequent occurrence as a result of climate change.
