The Federal Environmental Office said the female fish was photographed and then released to the river, Swissinfo reported.
Olivier Schmidt, an employee of the Natural History Museum in Basel, happened to be in the area when Thomas Wanner caught the salmon last week in the Birs.
"We could hardly believe our eyes," Schmidt said. "A salmon in the Rhine or was the around 90-centimenter- (almost 3 foot-) long fish simply a rather large trout?"
Salmon that come up the Rhine from the Atlantic have a long journey before reaching Switzerland and one with many barriers, including hydroelectric plants along the river. But Erich Staub of the Federal Environmental Office said the countries along the Rhine have made great progress in cleaning up the Rhine in the past 20 years.
"The River Rhine has been ready for salmon coming back for at least 10 years so water quality is not a problem," Staub said.