The Atlantic Salmon Federation says only about half of the young salmon in New Brunswick are making it through estuaries and out to sea.
The federation shared its research with more than 130 scientists at a meeting of salmon researchers in France this week.
Every year the Atlantic Salmon Federation tags 80 young salmon, also known as smolts, with transmitters.
The Federation is able to track which smolts make it down river successfully. It can also pinpoint where along the river the smolts get into difficulty.
It has been tracking the young salmon since 2005.
Jonathan Carr is the federation's director of research and environment. He said the fish that were tracked tend to do well in fresh water, but only 50 per cent make it to open sea.
"What we have found is there's a really high mortality in the estuary areas like the Miramichi Bay and the Bay of Chaleur," he said.
Carr says the goal now is to figure out what's happening to the other half, but it's difficult to tell what's killing them.
"It could be predators possibly striped bass in the Miramichi system, it could be cormorants [in] Restigouche, things like that. What we have to do now is narrow that down. That's the next step," he said.
Other possible culprits could be pollution or exotic species.
Protecting young salmon
Carr said until the problem is identified, the government should do more to protect salmon using tougher regulations around buffer zones and pollutants.
According to past estimates, Carr said in a good year the smolts have about a seven to 10 per cent survival rate.
"So for every 100 smolts leaving, you would typically get anywhere from seven to 10 smolts coming back," he said.
But he added in recent years, research has found as few as less than one per cent of smolts coming back.
Carr says if the mortality rate in estuaries can be reduced and more young salmon make it to sea, there is a better chance the population will rebound.