The new study found that acidification of rivers could make young pink salmon, the most abundant type in the Pacific, smaller and more vulnerable to predators by dampening their ability to smell danger and slowing their early growth.
In the Canadian experiments, pink salmon grew on average to only about 32 mm after 10 weeks, when raised in waters with roughly double current carbon dioxide concentrations, as expected in 100 years.
That was shorter than the 34 mm in waters with current levels. The young fish also weighed less and appeared less able to smell danger.
Furthermore, damage done by acidification "in fresh water in pink salmon could occur in all other salmonids", Colin Brauner, a co-author at the University of British Columbia, told Reuters.
Brauner said it was too early to say if the disruptions would last into adulthood and mean smaller commercial catches.
Carbon dioxide, the main greenhouse gas caused by burning fossil fuels, reacts with water to produce a weak acid. That especially threatens creatures ranging from oysters to lobsters which find it harder to build protective shells.
An international study in 2013 said acidification of the oceans was happening at the fastest pace for 55 million years, because of human greenhouse gas emissions.
Scientists say it is unclear how far salmon, and other marine life, may adapt or evolve in future generations to cope with rising levels of carbon dioxide.
In the past, the impacts of rising carbon dioxide levels have been studied in the seas more than in fresh water, yet 40 per cent of all fish are freshwater, said Brauner.
"We need to think about how carbon dioxide is affecting freshwater species," he said.