The first survey in 25 years of the river Suir and its tributaries has found significantly improved water quality.
Dr Martin O'Grady, of the Central Fisheries Board, who carried out the survey, said "a lot of damage has been reversed" on stretches of the river which had been "very polluted".
He believes the improvement is largely due to the construction of new sewage treatment plants and the upgrading of others.
This summer the Environmental Protection Agency (EPA) noted that the pearl mussel, a protected species regarded as "a sensitive indicator of water quality", had become extinct in the Suir during the past 25 to 30 years.
The EPA also named the Clodiagh, a tributary of the Suir, as one of the rivers which "had seriously polluted stretches in 2003-2005".
However, the findings of the new survey reveal that the Suir is slowly being rehabilitated.
Dr O'Grady recalled "standing in waders in a grossly polluted, virtually fishless river" near Holycross 25 years ago, but "today it is wonderfully pristine".
He said "one of the pleasant surprises" was finding "very large trout". He described the Suir as "the best brown trout angling river in the British isles which should be marketed to attract more tourists to the area".
While the survey found that stocks of juvenile salmon "are very similar to those recorded in the 1980s", Dr O'Grady believes "there are not enough salmon returning to the river from the Atlantic".
Last January the National Salmon Commission said salmon stocks on the Suir were 50 per cent below their conservation limit, and called for a ban on all salmon fishing "until a significant rebuilding of stocks takes place".
Despite its "potential as Ireland's greatest salmon river", anglers in 2005 landed less than 1,000 salmon on the Suir compared to 7,000 on the Moy and 1,700 on the Munster Blackwater.
Launching the results of the survey in Clonmel, Co Tipperary, last night, Minister of State for the Marine John Browne said "successive Irish governments have long since recognised the value of the inland fisheries sector to our economy, and significant investment has been made through the fisheries boards to ensure its conservation and protection..."
The Southern Regional Fisheries Board, based in Clonmel, which is the statutory body responsible for managing and conserving fisheries on the Suir, called for extra Government funding to undertake further improvements on the river.