He also added a bronze in the 1,500 metre freestyle.
He then competed in his first ever open water swimming event, finishing 18th in a gruelling 10km race in the Seine.
Wiffen has now confirmed he became "very unwell" following the race on his social media.
He said on X: "Thanks everyone who reached out, I’m incredibly disappointed to miss out on the opportunity to be flag bearer last night.
"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.”
After his first open water swim, Wiffen told RTE it would be his "last" time competing in the event and said "It was one of the worst things I've ever done."
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He then said he intended to "retire from open water" but appeared to blame the toughness of the event for his decision rather than the Seine's water quality.
The river's water quality was a huge talking point both before and during this year's Olympics.
Back in July, triathlon training sessions in the Seine were canned, which led many athletes to believe the swimming in the river wouldn't go ahead.
The actual event was then delayed several times due to elevated E.coli levels before swimming in the Seine was officially given the go-ahead.
Swimming in the Seine had been banned since 1923 but beginning in 2015, France launched a massive cleaning operation costing over £1billion to ensure water quality levels would be ready for the Olympics.
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