Organisers had to cancel training this week in the river and postponed the men's race on Tuesday after the Seine was found to be too dirty for athletes following heavy rainstorms last week.
World Triathlon and the Paris Games' organising committee announced around 4:00 am (0200 GMT) on Wednesday that the women's race would go ahead, followed by the rescheduled men's event.
"The results of the latest water analyses, received at 3.20 am, have been assessed as compliant by World Triathlon allowing for the triathlon competitions to take place," said a statement.
Rain fell overnight in Paris, but had stopped by the time athletes jumped off a pontoon laid over the river at the historic Alexandre III bridge in the heart of the City of Light.
The race started with a 1,500-metre swim in the Seine, with swimmers doing two laps in the river, with and against the current.
Flora Duffy of Bermuda, who took gold at the 2020 Tokyo Olympics, led after the first lap.
