The fish were found floating in the Allan Water, upriver from Dunblane.
The Scottish Environmental Protection Agency was called in amid fears the fish could have been poisoned, but said they believe a change in water conditions could be to blame.
Anglers have said the loss is "significant" and could affect fishing on the river.
A spokesman said Sepa had investigated after reports of dead fish in the water near Dunblane and Braco, and had found no evidence of pollution which could have contributed.
He said: "Sepa officers have carried out an inspection of the river and believe the incident could have been caused by stress due to low flows in the watercourse during the migration offish upstream."
Roy Robertson, chairman of the Allanwater Angling Association, said that the loss was "significant".
He said: "Losing that amount of fish is always a concern. They are worth a lot of money, and losing 100 salmon in the river will definitely have an effect."
Stress due to low water in a Perthshire river has been blamed for the death of more than 100 wild salmon.