A report by Scotland's Centre of Expertise for Waters (Crew) found that 97% had seen an increase in temperature between 2015 and 2019.
The researchers have warned that the changes create a greater risk of harmful algal blooms developing.
The Scottish government said it was "vital" that more action was taken to tackle and adapt to global warming.
The report says that most lochs and reservoirs in Scotland warmed by between 0.25C and 1C per year over the four-year period.
However, the temperatures in 9% of them increased by 1C to 1.3C per year.