Solely based on semantics, I would say that an acidic estuary is characterized by water having low pH values (lower than the usual 8 of seawater). This means that low pH may be a feature of the estuary.

An acidified estuary, on the other hand, may be an estuary that under normal conditions would have 'normal' pH values (close to seawater), but has been under some pressure that perturbed the pH balance. The result would be a decrease in pH. This can occur over a long period of time, or can be the result of an accident, etc.