According to the study by more than 150 Government and university scientists, global warming could cut commercial fish catches around Scotland by 20% while they increase by 10% around the south of England.
Gradually rising temperatures caused by climate pollution could drive porpoises, whales and dolphins away from Scotland's shores, it says, and the sea will become increasingly acidic, which could harm marine wildlife.
The Marine Climate Change Impacts Partnership has released its report card for 2013. It summarises the latest research from 55 UK science organisations including Scottish Natural Heritage, Marine Scotland and the Scottish Environment Protection Agency.
"This is a worrying report and confirms that major changes are coming for Scotland's marine environment, with water temperatures and acidity rising, and important fish stocks and wildlife on the move," said WWF Scotland director Lang Banks.
The fishing industry commended the study, but sounded caution. Paul Williams, chief executive of industry body Seafish, noted the report showed low confidence in its conclusions, but added: "Nonetheless it is important to understand any potential scenarios as clearly as possible, and having worked with many of the contributors to this report on a range of environmental issues over the years, we'd be keen to engage on behalf of the seafood industry."