Following a meeting "on the water quality" and tests, "a joint decision was taken to cancel the swimming part of the triathlon orientation," a Paris 2024 and World Triathlon statement said.
The River Seine was declared clean enough for swimming in tests from mid-July, but doubts remained as to whether the waters would be fit for competition.
"Paris 2024 and World Triathlon reiterate that the priority is the health of the athletes. The analysis carried out yesterday in the Seine showed water quality levels that... do not present sufficient guarantees to allow the event to take place," the statement said.
Organisers blamed rain in recent days and said they were "confident" water quality would improve enough before the triathlon competition is due to start on July 30.
In the event of heavy rain, untreated sewage can be washed into the river.
If the quality is below standards a "Plan B" involves postponing the events for a few days or moving the marathon swimming to Vaires-sur-Marne, on the Marne river east of Paris.
On July 17, Paris Mayor Anne Hidalgo swam in the Seine along with Paris 2024 chief organiser Tony Estanguet.
