A natural swimming pool doesn't use chlorine to keep itself clean, instead relying on plantlife and beneficial bacteria to keep the water clean. Plants are kept in a nearby pool called the "regeneration zone." This is full of plants and bacteria that absorb harmful nutrients. Water is pumped from the swimming zone into the regeneration zone. Here, it's naturally filtered of negative chemicals and nutrients before being pumped back into the swim zone.
Water in a natural pool is constantly circulating so that the swimming zone has constant acces to freshly filtered water.