Thousands of bridges, weirs, culverts and other barriers will have to be removed or altered to allow rivers flow freely from source to sea.
Almost 75,000 man-made barriers are stopping the natural movement of the country’s rivers, creating lethal conditions for fish and other wildlife.
More than 10,000 are causing significant problems and need to be taken away or reconfigured.
Just 257 have made it on to a works list so far, however, and politicians have been told it will take 50 to 60 years to fully tackle the problem.
Representatives from the state agency Inland Fisheries Ireland, and voluntary groups the Irish Trust and the Atlantic Salmon Trust, stressed urgent action was needed.
Barriers trapped fish, interrupted water flow, prevented nutrient and sediment dispersal, caused overheating and created crowding that spread disease, they said.
Migratory fish such as salmon, sea trout, lamprey and eels that travelled between rivers and the sea were particularly at risk.
Other species such as pike, bream and brown trout that covered long distances within rivers were also harmed.
“Having to pass multiple barriers in a river system has a cumulative impact on migratory fish, using up valuable energy reserves to pass each one,” Mark Horton, of all-Ireland group the Rivers Trust, told the Oireachtas Environment Committee.
“Fish can often suffer significant injury or direct mortality as they continually throw themselves at these human-made barriers to fulfil their natural migratory instinct,” he added.
The iconic Atlantic salmon has suffered so much that just 150,000 survive to spawn in Irish rivers each year compared to 1.7 million 30 years ago, he said.
“Barriers to successful migration to the sea and subsequently accessing vital spawning habitat on their homeward journey is a significant contributing factor,” he said.
Kris Murphy, of associate group, the Slaney River Trust, said at one weir, fish regularly got trapped and had to be stunned by electric shock, scooped into barrels and then released upstream.
“There is mortality associated with that,” he added.
He said that the trust had spent seven years trying to get the necessary environmental reports carried out to seek permission to install a protective grid which was a huge burden on a local voluntary group.
Inland Fisheries Ireland chief executive Francis O’Donnell said even though the organisation was a state agency, it also faced difficulties getting remediation carried out.
The new National Barrier Mitigation Programme had identified 73,377 bridges, culverts, sluices, weirs, dams and dredging and drainage channels in need of assessment.
Outdated laws, issues over private land ownership and conflict with other state agencies were all creating difficulties.
He said some dredging and drainage being carried out by the Office of Public Works for flood relief were “kneejerk reactions”.
Mr O’Donnell agreed with the committee chairman, Brian Leddin, that works under way at the Newport River in Co Tipperary would be “devastating” for habitats and species.
“The reality is if a town or village gets flooded two or three times, something has to be happen in terms of mitigation (of flood risk) but it’s about getting the balance right,” he said.
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