It is hoped findings from Operation Ocean Witness, a joint project between Scottish marine charity Open Seas and Greenpeace UK, will help guide decisions on how fishing activities are managed in the future.
The research cruise around Scotland follows a similar study in the English Channel last year, which gathered evidence on the impacts of industrial fishing.
The expedition is beginning on the east coast, setting off from Berwickshire, and cruising northwards.
The Sea Beaver and crew will make pit-stops at both large ports and small harbours on their journey, before heading south around Scotland’s west coast later in the summer.
They plan to meet with communities across the country where work is being carried out to safeguard the local marine environment.
Phil Taylor, head of policy and operations for Open Seas, which campaigns for sustainable fisheries, said: “The environmental health of our seas is below the waves, out of sight and sadly often out of mind.
“We hope this project will help raise awareness about the current condition of our seas.
“Our coastal seas are massively important for the wider functioning of our marine environment, holding precious nursery grounds for fish and other marine life.
“Unfortunately, our coastal seabed and inshore fisheries are under pressure and the harbours that once supported hundreds of small fishing boats are now empty or in decline.
“Everyone agrees we need more research and more knowledge about what is happening in our oceans – we hope to be able to provide some of that.
“There is a huge opportunity to regenerate nature in our seas and make our fisheries more sustainable.”
Fiona Nicholls, oceans campaigner at Greenpeace UK, said: “We’re so excited to see Operation Ocean Witness head north for Scottish waters.
“After a brilliant summer patrolling the English Channel last year, documenting and investigating industrial fishing, it’s time for Sea Beaver to investigate the health of Scotland’s seas and push Holyrood and Westminster to take proper action to protect our oceans.”