The fountain in Northampton’s Market Square has been switched off after tests revealed high levels of legionella and other bacteria.
The news comes after calls to the Herald & Post claimed the fountain was infected.
However, the council told the H&P on Wednesday it was turned off because of “high winds”.
Legionella, in some people, mainly older folk with compromised immune systems, can lead to legionnaire's disease.
This can be caused by breathing in bacteria when it is dispersed into the air in fine drops of water.
The move follows routine testing by a specialist company who check on the fountain monthly - a much more stringent testing regime than good practice recommends, according to Northampton Borough Council.
Work is now going on to disinfect and retest the fountain before it will be switched on again.
The council will also be investigating how the raised levels occurred so that if possible, action will be taken to stop it happening again.
The council says this rigorous approach to monitoring is taken to ensure the safety of the public, and means that traces of bacteria are picked up at very low levels so that action can be taken immediately to minimise any risk to health.
Councillor Tim Hadland, cabinet member for planning, enterprise and regeneration, said: "This is very frustrating as we know how much people enjoy the fountain in the warm weather.
“Our monitoring and testing regime is particularly robust as public safety is absolutely paramount and we will take no risks. We'll put the fountain back on as soon as it is retested and the results have returned to normal."