The INNS project has been established to tackle both non-native plants and animals - Japanese knotweed, Himalayan balsam, giant hogweed, American mink and signal crayfish.
The project is part of SEPA's Dumfries and Galloway Catchment Management Initiative, to establish a control programme in the Nith and Annan areas.
Two project officers from the Annan and Nith District Salmon Fishery Board will work in conjunction with the Criminal Justice Community Service programme to tackle the issue. The project will coincide with work done by the Galloway Fisheries Trust on smaller rivers in the area.
SEPA South West operations manager Robert Kerr said: "The issue of invasive species is a national one, threatening biodiversity across the UK. Their ability to aggressively colonise many areas has resulted in damage to our environment, the economy, our health and the way we live."
The project has been part funded through SEPA's Restoration Fund, LEADER Dumfries and Galloway and Patersons Quarries.