More than 560 SEPA employees have been given three months to sign up to new pay grades. If they do not they will be dismissed.
Unison said staff are discussing strikes. SEPA would not be drawn on how its work in such areas as floods, contaminated land and waste would be affected.
A SEPA spokesman said it is considering the implications but will not know the number of losses until June. He stressed that no jobs are being axed.
The three-month notices come with an offer of contracts containing new conditions. Ten per cent of staff will have pay frozen as SEPA aims to simplify pay scales and meet equality laws.
The spokesman insisted that many low-paid staff would enjoy better salaries. He confirmed that 769 staff have accepted the conditions. He added that the new system maximises the funds available in the pay remit set by government.