The Health and Safety Executive (HSE) launched an investigation in November 2016 after the visitor to the Walton-on-the-Naze Lifestyles centre fell ill and was hospitalised.
Tests showed the showers and fitness room at the council-owned complex contained legionella bacteria, the BBC reported at the time.
Ian Davidson, chief executive of Tendring District Council, confirmed that the local authority is to be prosecuted, but said its systems for managing the risk of legionella have been upgraded since the incident.
He said: "As soon as we became aware of the presence of legionella bacteria at the new facility at Walton-on-the-Naze Lifestyles we moved to address the issue immediately, with the centre closed for three months while remedial works took place.
"Our investigation was quickly widened to include a review of our systems and practices right across the council and, working alongside the HSE, these are now extremely rigorous.
"It would be inappropriate for me to comment further about this specific incident and the charge ahead of the court case," he added.
A hearing is scheduled to take place on 6 December.