The writer has used a plural form of 'water' with an 's'', so you need to use the plural verb form:
'The waters are very shallow.'
or 'The water is very shallow.'
Although, in general, 'water' is considered to be uncountable, in a few phrases, such as 'the waters of the Nile', 'the waters of the Ganges', it can be treated as a countable noun.
Student or Learner