I live in Australia and every source of water I've seen -- be it river, lake, billabong or creek -- has been a uniform shade of brown. How did the Indigenous Australians (and, by extension, the early European settlers) find clean water to drink?
Not a historian, but since no one has commented yet I shall chime in.
Australian plants as Aboriginal Tools by Phillip A Clarke gives a pretty detailed description of water gathering using plant materials. Stuff like sponges made of plant material, long reeds to access water in deep holes, water lily stems with leaves as filters. Soruces include deep rock crevices, hollowed out tree trunks, watering holes in rock, etc. Once a watering hole has been found, they are often covered to prevent evaporation, algae growth, and pollution from wild animals.
Banksia flowers were also used as filters.
Lastly, as I understand it, the aborigines would've spent most of their time near wateringholes or near the coast/rivers. Australian plants as Aboriginal Tools has a whole section on the boats they made to use on these bodies of water.