But renewable energy developments will still be run from London, in a bid to keep investment rolling in.
Ministers slammed the UK-government-led proposals as a "missed opportunity for much needed accountability".
The rights to fish for wild oysters and mussels in Scotland will be transferred to other parties, while some land at West Princes Street Gardens will be given up.
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The Scottish Affairs Committee at Westminster reported that Crown Estate powers should be devolved to local communities for increased transparency.
But the UK government responded that it was "not persuaded", and argued that a "unified management framework" would attract more investment in offshore renewable energy.
The Crown Estate owns the rights to renewable energy developments, ports and marinas as well as fish farms.
In this raft of reforms, new senior managers will lead operations in Scotland from Edinburgh.
The Crown Estate's Scottish Commissioner, Gareth Baird, said: "The reforms we are announcing today acknowledge that we could have been more responsive to local communities in the past."
But Rural Affairs Secretary Richard Lochhead said the developments "do not go far enough".
He said: "While it's encouraging that the Crown Estate is taking steps to be more responsive to the needs of local communities, it is still the case that Scotland’s communities stand to see no direct benefit from the exploitation of our vast natural resources."
(NE)
