Near the towns of Shahrtuz and Qubodiyon you will find the lower Kofarnihon River. It is a usually brown and muddy river that appears to come out of the mountains. You will see local kids swimming in it all the time.
But this river has a secret. It does come out of the mountains through a narrow canyon, but travel upriver through that canyon and you will eventually get to Dushanbe. Much of the water in this river has been through Dushanbe, and includes run-off from the city and waste water. This is in addition to run-off water from large agricultural operations and fields. I don’t swim here.
You will find a similar situation with the lower parts of the Vakhsh River. At the town of Qizilqala (Kyzylkala) the blue Vakhsh is joined by a very muddy tributary river that has gone through all the farms in the Yovon Valley. Also, by this time the Vakhsh River has gone past some factories, fish farms(?) and large farming operations. I wouldn’t swim downstream from the bridge over the River Vakhsh.