Action beginning May 12 could restrict Sepa's ability to carry out work relating to sampling, inspection and flood warning.
Out of 510 Unison union members 448 (87.8%) voted in favour of action short of a strike.
The vote comes after 40% of staff were given three months notice by the publicly-funded body unless they accept new terms and conditions.
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Sepa have said new arrangements would see 90% of staff would receiving pay increases but about 130 employees will not receive rises in the near future.
According to Sepa pay will be "temporarily held back in order to bring their salary within their new pay grade."
Sepa have put the changes in conditions down to equality legislation.
John Keggie, Unison's Scottish organiser, said: "This is a clear rejection of management's attacks on staff pay and conditions and we would hope that Sepa will see sense and withdraw their threats of imposition.
"We are always available for discussions with the employers, but staff are deeply frustrated and need more than words."
(GK/JM)
