The trash has collected in the basin outside cafes, bars and restaurants at The Shore as a boom prevents it from entering the docks beyond.
It is a problem local residents say has been ongoing for decades, but has come to a head after storms hit the capital at the end of June.
Jim Jarvie, from the Friends of the Water of Leith who has set up a petition in his latest fight to get the rubbish removed, said the main problem is that no one is taking responsibility for the mess.
He added: “There used to be a working group that cleared the water but that fell apart. The council say it’s not their problem because Water of Leith 2000 own the water, but Water of Leith 2000 say it’s not their problem because the rubbish comes down from the rest of Edinburgh.
“They say it’s just a freak accident that we are seeing now. The day after the storm it was much worse than usual. It hit the boom and went back five or six metres, and now it’s swirling around the basin. It looks appalling. We need action.”
Water of Leith 2000, who runs the basin and collects fees from barges docked there to maintain the area, did not reply when approached by the Evening News. But in an email seen by the newspaper, managing director Ron Kitchin said the matter was “very much in hand”.
It reads: “This was, as you are probably aware, all due to an exceptional flash flood causing a huge rise in the depth of the water of Leith. Both the council and Forth Ports are working with specialist contractors and awaiting proposals for the removal of everything at one central point.”
John Tindal, who runs the pub Teuchters Landing , said he understands the storm was exceptional, but it has taken too long for the rubbish to be cleared.
He said: “I understand there has been a storm and there is going to be more, but we do get an awful lot of crap. It just floats from one side of the basin to the other. It would be nice if there was a programme to clean it up once a month. It’s a shame. Nobody seems to care.
“When the wind blows or the tide turns, it’s just a sea of crap. We’ve got a boom that goes across and protects the pontoon from all the rubbish, but people are sat there having a drink looking out on this sea of crap. It happens all the time. ”
Edinburgh City Council are helping to organise removal of the rubbish and said they want to find a long term solution.
Council leader Adam McVey said: “Recent flooding has exacerbated the problems at the basin and in response we’re stepping in to help organise a specialist contractor to clear the debris.
“We’re working closely with the owner of the water basins, Water of Leith 2000, to help them meet their responsibilities and with Forth Ports, who own and manage the docks, to address the issues here and we fully understand and empathise with residents’ frustration. The Shore is a fantastic asset for Leith and the city and it’s imperative we all work together to look after it properly so it can be enjoyed by everyone, as well as kept clean and safe for local wildlife.”