Eagle Wharf wharf in the London Borough of Hackney is listed as a building of local architectural and historic interest and is in the Regents Canal Conservation Area.
But developers want to knock down some of the former industrial buildings to create new flats, commercial space and a cafe.
The council received objections from photography studio Holborn Studios Limited, and many others, but granted planning permission in November last year.
Holborn Studios and Del Brenner, a member of the mayor of London's Waterways Commission, then mounted a judicial review challenge.
And on Friday, Judge John Howell QC ruled they had not been fairly consulted about changes to the scheme.
Freeholder, GHL (Eagle Wharf Road) Limited, "substantially altered" its planning application, initially lodged in 2015, in May last year, the judge said.
Among other things, the mix of proposed uses was changed, the number of residential units was cut and all the affordable housing units were deleted.
But Hackney Council did not consult either Holborn Studios or Brenner about the changes, London's High Court heard.
They should have been given an opportunity to express their views about the changes "as a matter of fairness", said Judge Howell.
Holborn Studios, Brenner and others had been "deprived of a fair opportunity to make representations" to the council.
"The procedure followed in the circumstances was so unfair as to be unlawful", he ruled.
And, overturning the planning permission, the judge found that, had objectors been given a proper say, the outcome could have been different.
The court heard earlier of Holborn Studios' concerns that space provided for it in the new development would not meet its needs.
It feared that "the existing cluster of creative and media firms" occupying the wharf would be "driven out" by the development.
Brenner is secretary of the Regent Network, a community organisation that aims to protect London's waterways from inappropriate development.
R on the Application of Holborn Studio Limited v London Borough of Hackney. Case Number: CO/6434/2016