Northampton Borough Council has not specified the amount of legionella found in the water.
Official figures show there have been 13 cases of patients catching the legionella bacteria since 2002.
The disease is a potentially fatal form of pneumonia caused by the legionella bacteria.
The Legionella bacteria is commonly found in sources of water, such as rivers and lakes.
Potentially deadly legionella bacteria have been found in showers at a community centre in Dundee.
Pascal Bates, from the HSE, said the hospital's procedures on legionella fell "markedly short".
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Legionella bacteria can contaminate and grow in other water systems such as cooling towers and evaporative condensers.
The death is the third in nine years at Basildon University Hospital linked to the legionella bacteria.
Water restrictions at a Lincoln sheltered housing block where Legionella bacteria was found have begun to be lifted.
She said a joint legionella review has been produced by the hospital in partnership with other health organisations.
It said there had been a history of people catching legionella at the hospital, citing 13 cases since 2002.
The report, she said, concluded the current risk of contracting legionella at the hospital was about "one in a million".
The single charge from the HSE relates to cases of legionella at the hospital between February 2004 and December 2010.
The prevention and control of legionella at an Essex hospital remains a "significant concern", according to a health care watchdog.
He said steps were being taken to ensure more Health and Safety Executive inspections of potential legionella sites were carried out.
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It added a legionella management group met once a month and the hospital worked with several other agencies regarding the outbreaks.
Last-minute changes to the design of part of the hospital site have now been cited as a possible cause of legionella there.
Earlier this year three people died in a legionella outbreak in Edinburgh.
There have been 12 inpatient legionella cases at Basildon Hospital since 2002.
Water restrictions will remain in place at a Lincoln sheltered housing block where Legionella bacteria was found, for at least another three days.
The bacterium legionella pneumophila and related bacteria are common in natural water sources such as rivers, lakes and reservoirs, but usually in low numbers.
The fountain, located in the market square, was switched off last week after "higher than normal" levels of legionella were found in the water.
Last-minute changes to a hospital building might have played a part in the spread of legionella which caused two patients' deaths, it has emerged.
People become infected when they breathe in air containing legionella bacteria.
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Finally it needed to make sure premises are safe from legionella infection by taking action set out by the Health and Safety Executive by 2 August 2010.
The report said the hospital had made an "investment in measures to control legionella" including the introduction of a silver and copper ionisation disinfection system, to replace its chlorine dioxide one.
"The trust has not had any cases of Legionnaire's Disease since 2011 and we will continue to work with the HSE and other experts to do all we can to combat Legionella, " she said.
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