The £45,000 contract will help establish minimum three-hour flood warnings for the Elgin and Angus areas of north-east Scotland and the Borders.
It is part of a larger project funded by the Scottish Government to provide an active dissemination service across the country by March 2011.
Entec will also collate data to develop the forecasting models for SEPA's warning systems. Project manager Steve Anderton said: "This will help emergency planners in local authorities provide a more effective response."
SEPA principal hydrologist Michael Cranston said: "This work will allow us to deliver more targeted information to communities in Moray and the Borders, including Elgin, Forres, Hawick and Newcastleton."