The warning came from Fife Sports and Leisure Trust as it worked to ensure it had sufficient supplies to keep its facilities open.
It runs pools across the Kingdom.
The charitable trust said it is in close contact with suppliers, and pools remain unaffected - but the numbers using them is expected to rise during the busy summer months.
The shortage is being attributed to a fire at a major supplier in the US, disruptions to supply chain caused by Covid and ongoing worldwide transportation issues which is now affecting the leisure industry across the UK.
Emma Walker, chief executive, said: “We are notifying customers of a potential, short-term issue with regards chlorine supply and we are working hard to ensure we maintain supplies to keep our pools across the region open.
“We are hopeful that with our current level of supplies and our operational team working collaboratively with our supplier, we will keep pools open without affecting customers and our summer programme for juniors.
“We feel it’s important to share information with customers and we will be updating our website and social media regularly with any updates.”
Paul Vaughan, Fife Council's head of communities and neighbourhoods said: “We are working to keep school and community use pools up and running and is closely monitoring the situation.”