The non-native bait fish ruffe can now be found in Loch Lomond
Legislation making it illegal for fish or live spawn to be introduced to inland waters without permission has been announced at Holyrood.
Environment Secretary Richard Lochhead said the new rules would provide greater protection from alien species.
Loch Lomond now contains ruffe, a small bait fish not previously present, while another non-native fish, carp, has been found in the Clyde.
The regulations will come into force on 1 August.
Mr Lochhead said the Scottish Government had already taken steps to limit alien invaders through the non-native invasive species strategy, launched earlier this month.
He added: "The legislation I am announcing today provides the government and district salmon fishery boards with a powerful tool to protect Scotland's unique and fragile freshwater biodiversity, while continuing to promote the world-renowned fishing it supports."
Depending on the river concerned, responsibility for the applications will rest with either district salmon fishery boards or Scottish ministers through the Fisheries Research Services (FRS).
Officials will need to be satisfied there is a case for stocking fish and that they do not threaten native Scottish species before permission is granted.
The new regulations were brought in via the Agriculture and Fisheries (Scotland) Act of 2007.