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The pipes – known as combined sewer overflows (CSOs) – discharge sewage into the river as a relief for the system when there is particularly heavy rainfall or flooding.
But Scottish Water acknowledges they are not monitored, so there is no data showing how often there are sewage spills or how serious they are.
Jim Jarvie, of campaign group Save Our Shore (SOS) Leith, said news of the 25 outflow pipes had come as "a big surprise".
"We knew there were a couple which had been leaking over the last couple of years, but we had no idea it was a number like 25 – that was a complete shock,” he said.
He said SOS Leith was already concerned about the rising level of silt in the river and the bits of wood and other rubbish trapped there.
"This is one more issue around the mismanagement of the water down here. It's more filth coming into the river and causing who knows what kind of health issues as well."
Leith Labour councillor Gordon Munro, who obtained the information about the CSOs from Scottish Water, said: “I would have thought the days of using the Water of Leith as a sewage pipe were long gone but it appears not."
South of the border, Feargal Sharkey, former lead singer of punk band the Undertones, has highlighted a 37 per cent rise in raw sewage discharged into English waters in a year and described government inaction on rivers as an act of "global hypocrisy" with the COP26 climate summit taking place in Glasgow.
Figures released in the summer showed in Scotland, based on what data was available, there had been a 40 per cent increase in sewage spills in the past five years, with the equivalent of 47,000 Olympic-sized swimming pools worth of waste discharged since 2016.
Mr Jarvie said before Forth Ports had built the lock gate in the harbour in the 1960s, restricting the tidal flow, the Water of Leith had been 20ft deep.
“Now it's a few centimetres and in some places there is silt exposed so we're worried about what that means for the health of the area – and to know now there's sewage leaking on top of that causes even more concern,” he said.
Councillor Munro said wildlife had started to return to the Water of Leith, with herons and otters spotted, but warned it could disappear again if sewage discharges continued.
“It is within the power of Scottish Water or the Scottish Government to change this practice and be an exemplar,” he said.
Scottish Water said CSOs were a controlled relief mechanism to prevent flooding in homes and businesses and sewage was usually combined with waste water from sinks, showers and baths and surface water from roofs and gutters.
A spokeswoman said: “The levels of untreated sewage in storm water that is discharged is very dilute so is unlikely to cause harm to the environment.”
She said Scottish Water was looking at a range of long-term options to manage storm water in a sustainable way, including a reduction in the pressure on infrastructure while still enabling growth in the city.