Macra has said a new report on the Nitrates Directive "reinforces the need for a balanced and practical approach to improving water quality".
This approach should recognise "both the progress made by farmers and the challenges that remain", the farm organisation said.
A review of the EU Nitrates Directive, which governs farm manure limits and the nitrates derogation, was published last week.
In the first official evaluation of the Nitrates Directive since it was adopted in 1991, the European Commission said that the current limit of 170kg of manure nitrogen (N) per hectare remains effective and scientifically sound.
The evaluation also identified the need for smarter implementation and improved delivery of measures on the ground.
Macra national president, Josephine O'Neill said: “Young farmers are fully committed to improving water quality and recognise that protecting our natural resources is essential for the future of both farming and rural communities.
"The European Commission's evaluation acknowledges that the Nitrates Directive is working, but it also recognises that achieving lasting environmental improvements requires practical implementation, investment and time.”
The organisation noted that young farmers "fully recognise the importance of protecting and improving" water quality.
They have invested significantly in recent years in measures such as slurry storage, low-emission slurry spreading equipment, protected urea and nutrient management planning.
Macra said the commission's findings underline the fact that environmental progress "takes time and that improvements in water quality are often subject to significant time lags before the benefits of on-farm measures become visible".
The organisation warned against portraying farmers as the cause of all water quality challenges, stressing instead that young farmers are "among the sector's greatest environmental champions and are committed to leaving the land in a better condition for future generations".
"Our members have made significant investments in better nutrient management, modern slurry storage and low-emission technologies, often at considerable cost," the organisation said.
"These actions demonstrate that farmers are part of the solution, but we need policies that support continued progress rather than placing additional pressure on farm families who are already delivering real environmental gains."
Macra reiterated that if policymakers are serious about improving water quality outcomes, they must "ensure that farmers have access to the infrastructure, advisory services and financial supports needed to deliver further improvements".
The organisation called for increased investment in the Targeted Agricultural Modernisation Scheme (TAMS 3) and other capital support schemes, particularly for nutrient storage, slurry management and water protection measures.
Macra also renewed its call for long-term funding commitments for successful initiatives such as the Farming for Water EIP, noting that certainty around funding is essential if farmers are to continue investing in environmental improvements.
Macra further emphasised the importance of ensuring that future water quality measures remain evidence-based, practical and proportionate, recognising the realities of farming on the ground and the need to maintain the economic viability of family farms.