The neon red text, which read “Resist the attempted silencing of Julian Assange,” was projected onto a black backdrop before the concert.
Waters, who is an admirer of Assange, has previously also featured images of the whistleblower in his shows.
Julian Assange has been living at the Ecuadorian Embassy in London since 2012 and for the past few weeks has not been allowed to use phones or the internet.
The new restrictions were enforced in March after the whistleblower broke a vow to cease all “political activity” by speaking out about the poisoning of Sergei and Yulia Skripal in Salisbury.
Waters, who is known to mix the world of music with politics, back in April denounced the Syrian opposition group the “White Helmets” while on stage in Barcelona.
“The White Helmets is a fake organization that exists only to create propaganda for jihadists and terrorists. That’s my belief,” Waters said.