Five areas in Cavan and Monaghan have been identified as areas needing improvements to prevent wastewater harming local rivers and lakes.
The EPA has prioritised 42 towns and villages across Ireland where there are pressures on surface water quality.
The ecological health of almost half of Ireland's surface waters is unsatisfactory because of pollution and other human disturbance.
Urban wastewater impacts 13 per cent of all low quality surface waters.
In Cavan, these areas are Bailieborough, Blacklion and Mullagh.
Castleblayney and Carrickmacross in Monaghan are also on the priority list.
In Castleblayney, upgrade works have been completed, with the EPA currently monitoring the treatment plant to see if the improvements are effective.
Irish Water is yet to give an estimated completion date for works in Blacklion, Mullagh and Leitrim, while the works in Bailieborough are now scheduled for 2025 instead of the previous target of 2022.
The recently published report also found that four Olympic sized swimming pools of raw sewage are being pumped into the Irish environment on a daily basis.
Environmental Officer with the EPA, Noel Byrne, says all of this is down to Irish Water underfunding water treatment facilities for years: