In a blow to Olympic officials who have repeatedly vowed that the Seine would be safe for athletes to swim in, organisers said the men's event would be delayed by 24 hours and take place immediately after the women's race on Wednesday.
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 local time (0130 GMT).
"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.
But 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.
French authorities have invested 1.4 billion euros ($1.5 billion) over the last decade to clean up the Seine, including in major new water treatment and storage facilities in and around Paris.
But 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.
The triathlon is the first Olympic event scheduled to take place in the river, before marathon swimming in the second week of the Games.
