Environmentalists have warned that Scotland's marine heritage is in "a shameful state".
Scotland boasts a large number of porpoises
WWF Scotland said coastal development, fishing, oil and gas exploration and aquaculture were taking their toll on the country's marine wildlife.
Its latest report said the UK's seas were in crisis due to poor planning and management by the authorities.
WWF said a UK Marine Act was needed to tackle the problems and safeguard endangered species.
The Marine Health Check 2005 report said that 13 of the 16 "flagship" species and habitats investigated were in decline.
A similar report five years ago warned of the dangers and these have largely gone unheeded, the charity claimed.
Scotland's waters are said to face the threat of pollution and the invasion of non-native species.
WWF Scotland's Helen McLachlan said the report illustrated that the plight of the country's marine wildlife were worse than originally feared.
"Our marine heritage is in a shameful state for a maritime nation," she declared.
"To most people, our marine environment is out of sight and out of mind, so its demise is hidden.
"However, it is not just our wildlife which is suffering from the current mismanagement. Coastal towns and villages in many parts of Scotland that once thrived on the riches of the seas are now experiencing hardship and economic decline."
'Crisis in our seas'
Scotland boasts one of the world's largest gannet colonies at St Kilda and 24 species of whales, dolphins and porpoises.
WWF Scotland said it welcomed Environment Minister Ross Finnie's recent commitment to a marine strategy for Scotland.
The number of harbour porpoises in Scotland has declined in recent years, while cod and salmon are also likely to have fallen, according to the report.
Environmentalists fear activities such as trawling and dredging have exacerbated the problems.
Ms McLachlan said that a UK Marine Act "would help solve the crisis in our seas" and transform the management of the marine environment.
She added: "Since marine management in Scotland has both reserved and devolved elements, WWF believes that the Scottish Executive needs to work with Westminster on the details of a UK Marine Act and align it with a Marine Act for Scotland, which will address the specifically devolved issues."