Irish rivers are more polluted today than 20 years ago, with major concerns that ramping up agricultural production could have a detrimental effect on water quality.
The Government has also admitted it is two years behind schedule in developing River Basin Management Plans (RBMPs) to improve standards, and that targets to achieve better quality have been missed.
The RBMPs set out how water quality can be improved and pollution reduced from wastewater treatment plants, agriculture, forestry and other sources.
A report detailing 'Significant Water Management Issues', published by the Department of the Environment, says that while overall quality is high, there are problems with compliance.
"This document outlines the current status of water quality in Ireland which, although it compares very favourably with water quality in other member states, falls well short of the targets set out in the first cycle of RBMPs," it says.
Among the major concerns include pollution linked to agricultural output, including use of fertilisers, pesticides and herbicides; effluent from wastewater treatment plants and septic tanks, forestry and industrial sources.
Agriculture is linked to 53pc of all pollution in rivers, and ramping up production under the Food Harvest 2020 strategy presents problems.
"Achieving the objectives of the Water Framework Directive in the context of increasing agricultural output will be a major challenge", it says.
"Increased agricultural output will likely increase the pressure on waters which will have to be managed in a sustainable way."
It also warns that increasing food output will result in a need for additional processing.
"The location of some existing processing sites could reach a limit where the capacity of receiving water is at or near capacity," it adds.
While steady progress has been made, "significant risks" remain, including increased output and a rise in emissions from wastewater treatment plants as the population grows.
The Environmental Protection Agency (EPA) said that increasing output would involve "intelligent management".
"It is a challenge," a spokesman said.
"We're seeing a stabilisation in water quality and Food Harvest comes along, and we can see a threat there if it's not managed correctly," he said.