Cleanliness test were also made just before the race. The article from apnews talks about them. I could only find french newspaper talking about it but the "heavy rainfalls" seemed NOT to be a problem.

L'orage de mardi soir "n'est pas passé loin", a admis mercredi le préfet de région Marc Guillaume, mais "il n'a pas plu sur la zone d'épreuves". En cas de précipitations intenses, de l'eau non traitée peut être rejetée dans le fleuve, un phénomène que les ouvrages de rétention inaugurés juste avant les Jeux ont vocation à empêcher. (https://www.europe1.fr/sport/jo-paris-2024-la-qualite-de-leau-de-la-seine-tres-bonne-lors-des-epreuves-de-triathlon-4260748)

Tuesday evening's thunderstorm "was a close call", admitted regional prefect Marc Guillaume on Wednesday, but "it didn't rain on the event zone". In the event of heavy rainfall, untreated water can be discharged into the river, a phenomenon that the retention structures inaugurated just before the Games are designed to prevent.