Untreated sewage is still being pumped into water at 44 locations - with Donegal and Cork accounting for nearly half of these areas.
A new Environmental Protection Agency report found wastewater treatment in over a quarter of Ireland's large towns and cities is below public health standards.
The report says 50 major towns and cities including Dublin, are failing to meet waste water treatment standards.
Meanwhile, Counties Cork and Donegal account for nearly half of the 44 areas where there's no treatment at all.
In 59 locations waste water is the sole pollution threat to waterways, with almost one quarter of these in Donegal and Galway.
The EPA says major investment is needed in our water treatment facilities if Irish seas, rivers and lakes are to meet environmental standards.