In a blow to Olympic officials who have repeatedly vowed that the Seine would be safe for athletes to swim in, organisers on Tuesday announced the postponement of the men's event.
A joint statement from Paris 2024 and World Triathlon blamed the excessive pollution on the heavy rain that deluged the French capital on Friday and Saturday.
"Paris 2024 and World Triathlon reiterate that their priority is the health of the athletes," the statement said after a meeting held at 3.30am.
"The tests carried out in the Seine today revealed water quality levels that did not provide sufficient guarantees to allow the event to be held.
"Unfortunately, meteorological events beyond our control ... can alter water quality and compel us to reschedule the event for health reasons."
Organisers had already cancelled training sessions in the Seine scheduled for Sunday and Monday because of unsafe pollution levels caused by last week's rain.
So what next?
Organisers on Tuesday said the men's event would only be postponed for 24 hours and would take place immediately after the women's race on Wednesday.
They had expressed confidence that the pollution would drop in time for Tuesday's race given the bright, sunny conditions in Paris this week which helps keep bacteria levels down.
However the weather is predicted to become unsettled again, with a weather warning for thunderstorms for Paris on Tuesday evening and the possibility of rain on Wednesday.
So what happens if it can't take place on Wednesday?
Organisers back in July revealed the 'plan B' for open water swimming events if they cannot take place in the Seine - two events are affected; the swimming section of the men's and women's triathlon and the men's and women's swimming marathon.
The triathlon is the first Olympic event scheduled to take place in the river, before marathon swimming in the second week of the Games.
The first step is to postpone and there is space within the Olympic schedule for both events to be postponed if necessary.
If, however, the water quality is still not good enough then there are two separate plans - the triathlon goes down to a biathlon in accordance with Olympics rules, meaning that athletes will only do the swimming and cycling stages and will be scored on those alone. The running and cycling events will take place within Paris as per the original plan.
The marathon swim, on the other hand, will be moved - it goes to Vaire-sur-Marne, a water park in the greater Paris region which is already hosting canoe and rowing events.
There were similar concerns about water quality at the Rio Olympics in 2016, with high levels of contamination revealed in the water in the days before the triathlon, but in the end the event went ahead with all three sections as planned.
What is the problem with the Seine?
French authorities have invested €1.4 billion over the last decade to clean up the Seine, including in major new water treatment and storage facilities in and around Paris.
The eventual plan is to open up swimming spots along the river in the city and suburbs for Paris residents, making one of the long-term legacies of the Games.
However, heavy downpours still overwhelm the city's underground drains and sewage system, leading to untreated effluent being released into the waterway.
After an exceptionally wet spring and start to summer, the Seine had been consistently failing water tests until the beginning of July, causing a major headache for Paris 2024 organisers.
Levels of the E.Coli bacteria - an indicator of faecal matter - were sometimes 10 times higher than authorised limits.
Friday - the day of the Olympics opening ceremony - saw torrential rain, while rain continued for most of Saturday, making the river much higher than is usual for this time of year.
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