The underlying window leak should be addressed, as well as what o1Marc said.
If not, expect the rust to rear its ugly head again in short order.
If it's any consolation, the rusted areas look minor and should clean up with good results.
When i firstly painted the floor it was stored covered. I moved it to a different location with non covered storage and thats when the rain leaked in. I now have it cover stored again. Also, I plan on removing the windows and raising the roof