Wiffen also won a bronze medal for Ireland competing in the 1,500m freestyle, before taking part in the challenging 10km swim through the River Seine.
Serious concerns had been raised throughout the 16-day Olympic competition about the state of the dirty water in the Seine, with daily measures carried out by Olympic officials to check for possible contaminates such as the bacteria E.coli.
The 23-year-old, who was born in Leeds, posted a message on social media thanking fans for their messages after missing the closing ceremony.
“Thanks everyone who reached out, I’m incredibly disappointed to miss out on the opportunity to be flag bearer last night,” Wiffen wrote on X, formerly Twitter.
“Yesterday I rushed to hospital as I was very unwell with a bug that I am being treated for, and am feeling better now. I hope everyone enjoys the evening and I hope to be well enough to seeing everyone when we get home.”
It is not yet clear what caused Wiffen to contract the bug, although he is not the first athlete to have swam in the polluted Seine River and later suffer from illness.
Three German swimmers were struck down after competing in open water races during the Olympics, although it hasn’t been confirmed that the swim was directly responsible for their sickness.
With Wiffen absent from the ceremony as fans gathered for the final event of the Olympics, Fintan McCarthy – who won gold in the rowing event – stepped in alongside bronze medallist Mona McSharry for Ireland at the closing ceremony.
McSharry and Wiffen became their nation’s second and third Olympic swimming medallists after Wiffen as Ireland secured seven podium finishes in Paris – their highest total to date.