A report from the Environmental Protection Agency (EPA) says around half of the waste discharges entering our waters do not meet pollution and health standards.
Untreated sewage is still being pumped into our seas and waterways from 38 towns and villages around the country.
Meanwhile, treatment plants in Dublin and Cork are among the 28 nationwide where discharges are below EU standards.
The EPA says years of under-investment in the system is one of the main causes.
But EPA spokesperson Darragh Page says Irish Water is not meeting its own targets for dealing with the issue.
"The level of investment by Irish Water isn't up to what they have said in their own investment plans," said Mr Page.
"So their own investment plan committed to spending an average of €326m per year on wastewater infrastructure and what we've seen is in 2017 they've spent €215m.
"Clearly, they're going to have to accelerate the pace of investment over the coming years to 2021 to make sure that they address the shortcomings that we are seeing in our report."