Hola Paul

You could have also used "el agua está clara", but I imagine the writer was thinking about an essential quality to that water, as if being always "clear, transparent", and that triggered the use of "ser" instead of estar. 

With the same argument we can say that the following sentence could also be using "es muy fría" if we consider this as something essential to that water (always cold).

Saludos

Inma