Many distilleries across Islay, Perthshire, and Speyside were forced to stop production during a summer of record temperatures.
Whisky is the UK's biggest food and drink export by some margin.
Some £2 billion ($3.85 billion) was shipped overseas in the first six months of 2021 - representing more than a fifth all food and drink sold abroad. The next largest export was salmon valued at £356m ($685 million), according to the Food and Drink Federation.
Carole Roberts from University College London said: "There's an assumption that Scotland is a wet, rainy place with a constant water supply.
"Climate change is changing when and where it rains, and this will create shortages and change the character of the water – affecting our favourite drams – so planning is essential to protect our whisky."
The Glengoyne distillery, which has premises in the highlands and lowlands of Scotland north of Glasgow, has created a wetlands facility for liquid waste.
Ahead of the UN Cop26 climate change summit, bosses are calling for greater support of wetlands, which capture carbon similarly to rainforests.
Barbara Turing, brand manager at Glengoyne Highland Single Malt, said: "The threat of climate change is very real, and we all have a role to play in combating its effects."