More water is likely to be discharged from the ESB's dams in the coming days as it looks to maintain the levels in its reservoirs.
The State electricity company has confirmed this is likely to cause even more flooding in Clare and Limerick, down stream of Parteen Weir.
Cork will also be hit by further floods when flows are increased on the River Lee.
The flow at Parteen was not increased yesterday, but at the Inniscarra Dam on the River Lee the discharge was increased to 250 cubic metres per second.
ESB engineering manager Tom Browne said releasing the water into the rivers is necessary to prevent flooding up stream. He said not releasing the water would have even worse consequences downstream.
The company uses the levels on Lough Derg on the Shannon to indicate when water needs to be released at Parteen.
"If we didn't do it, the level in Lough Derg would back up and ultimately you would get significant flooding upstream," said Mr Browne.
"You are creating a significant risk downstream then - because you would have a lot less room to manoeuvre if further heavy rain came," he added.
"The level in Lough Derg is our main operational criteria for that. The Shannon is quite a slow-moving river, so you could have rainfall in the middle or the north of the catchment and it might not find its way to Lough Derg for three, four or five days."
Many locals believe a build-up of sediment in the river is slowing the flow further, and exacerbating the damage caused by floods. In recent weeks, they have called for the Shannon to be dredged, to enable the water to flow much quicker.
However, Mr Browne said dredging the river would not have a significant effect.
"To be honest, I do not think that dredging is going to help us with the type of flooding we have at the moment," he said.
"The last large flood in the Shannon was in 2009. With a lot of heavy rain forecast, it is possible that we could get to those levels," he added.
Both the Parteen Weir and Inniscarra Dam are likely to see flow increases in the coming days as flood waters seep into the Shannon and Lee rivers.
"In relation to what is being discharged at Inniscarra at the moment, we expect there will be out-of-bank flooding, particularly in the western Lee fields and the west of the city," said Mr Browne.
"There will be some properties at risk, particularly to the west of the city," he added.