Developer New City Vision had applied for permission in principle from Glasgow City Council for the scheme at Govan Graving Docks.
The plans included 726 homes, a museum/heritage centre, restaurant, retail and office space and a hotel.
According to a document submitted to the council by the developer, the scheme would "see the ex-industrial and currently run-down site completely transformed with a mix of high quality homes and local amenities such as a hotel, shops, restaurants and office space".
"We believe that the transformational design will protect, celebrate and enhance the history, architecture and archaeology of Govan Graving Docks and the River Clyde for future generations", it said.
But Glasgow Council has refused the plans on 10 grounds, including that the scheme "fails to preserve the special architectural and historic interest of the Category A listed Govan Graving Docks".
A decision notice said the proposed development, "located within the functional flood plain, is generally not suitable for development and the proposal would not minimise flood risk".
It said that the site "has a significant probability of flooding and its development would also increase the probability of flooding elsewhere".
It also said that the applicant had "failed to justify the numerous tall buildings proposed in an area of sensitive urban character", and had "failed to justify the proposed residential density of the development with regards to the location, context and setting or the scale and massing of adjacent buildings as required by Glasgow City Development Plan guidance".