Passers-by were shocked to see the luminous water rolling through the city, with one saying it looked like a scene from hit 1980s sci-fi film Ghostbusters.
But the Environment Agency have moved to reassure residents, saying the colour is down to an environmentally friendly dye that is used to track the watercourses and river flows.
A spokesperson for the Environment Agency said: “The Environment Agency is investigating a green discolouration in Farnley Beck and a nearby lake, near Armley, following reports from members of the public.
"Our officers visited the area yesterday to assess the situation and it appears that the water contains a harmless tracing dye that is sometimes used for watercourse investigations.
“We have been working with Yorkshire Water to ascertain the source, and today we are carrying out tests on the water to ensure that it is harmless and poses no risk to wildlife. We are thankful to those who reported the matter to us. If anyone sees any pollution, they are urged to call our incident hotline on 08000 807060 so we can investigate.”
This isn't the first discolouration of a Leeds river.