Flags flew at half mast outside the Scottish Parliament that she helped to create and in which she served first as a member of the SNP and then as an independent MSP.
Graeme Brown, Director of Shelter Scotland, said: "Margo's years as director at Shelter Scotland from 1978-1981 were focused on helping people who were living in poor housing conditions, particularly in rural areas, and brought this to the public's attention in her customary style."
The Moderator of the General Assembly of the Church of Scotland, the Rt Rev Lorna Hood, said: "We join with all of Scotland in sadness as we hear of the death of Margo MacDonald.
"She was a larger than life character who transcended party politics and was fervent in her beliefs about Scottish independence. She was also passionate in her very personal campaign regarding the right to a dignified death."
Katherine Crawford, director for Parkinson's UK in Scotland, said: "Put simply, Margo was an inspiration to all she met and I am deeply saddened by her passing.
"It has been our honour to work with Margo over the last few years and we could not help but admire her bravery in living with Parkinson's."
Grahame Smith, Scottish Trades Union Congress General Secretary, said: "She was a passionate fighter for all she believed. You could disagree with her but never fall out with her and if she chided you it was always with a fair degree of humour."
Holyrood Presiding Officer Tricia Marwick, a former SNP MSP, said: "Margo was brave, passionate and committed. To be known and recognised by a first name is reserved to very few. But everyone knew Margo. She was a sparkling jewel in the Scottish Parliament."
Gordon Wilson, former SNP leader and colleague, said: "With her passing, much of the colour has gone from Scottish politics. It is a shame she did not live to enjoy casting a yes vote in the referendum."