Marine ecologists and oceanographers from the Scottish Environment Protection Agency (Sepa) are carrying out a four-week survey to check the condition of the water and improve scientific understanding of the environment.
Data and samples will be collected from locations along the west coast by the scientists on board the Sir John Murray survey vessel.
The boat is fitted with underwater HD cameras and a scanner which will allow the team to create maps of the various habitats and physical features found on the seabed.
The work will allow delicate environments to be better preserved while still letting people use coastal areas, Sepa said.
The first two weeks of the survey will see the Sir John Murray operating in Loch Linnhe and Loch Tuath, in Argyll, with the second half of the survey carrying out mapping and sampling work in Skye and the Western Isles.
Senior scientist David Ross said: "The survey is an exciting opportunity to really broaden our scientific knowledge of these coastal environments.
"We take what we can see in the world around us for granted, however until now getting maps and broad-scale knowledge of what lies beneath the waves has always been difficult.
"Using this data, we can better balance people's desire to use Scotland's coastal resources, with protection of these delicate ecosystems."
WWF Scotland director Lang Banks welcomed the surveys.
He said: "Scotland's seas and coasts are home to an amazing range of wildlife, but we need to see action to halt and then reverse the declining health of our marine environment."