The measures, the first of their kind in the UK, were introduced to replace the repealed European Shellfish Waters Directive.
A total of 84 shellfish water protected areas have been identified to continue supporting the expansion of Scotland's shellfish sector and to ensure a good-quality product which is safe for human consumption.
Steps will be taken to prevent the deterioration of water quality in these areas.
Environment and Climate Change Minister Paul Wheelhouse said: "The aquaculture and freshwater fisheries sectors are significant contributors to Scotland's economy as a whole as well as critical to the economies of many coastal and rural communities.
"Shellfish production is important for our rural and coastal communities and we recognise the need for clean water in these areas to ensure a high-quality product which is safe for human consumption.
"These new measures not only do that but significantly expand the area of water protected to enhance support for shellfish life and increase the number of high-class edible shellfish products.
"I am delighted that these are the next steps in our distinctive Scottish approach towards the achievement of a sustainable water environment."
Meanwhile, celebrity chefs and food experts joined forces to demand a Government crackdown on the illegal electrocution of shellfish around Scotland's shores.
Shocking the seabed forces razor clams out of their burrows so that they can be harvested easily. But it also kills marine wildlife.
Andrew Fairlie, who runs the only restaurant in Scotland with two Michelin stars, is among those who say it is being carried out by fishing boats out to make a fast buck.