Step 1: Read the active sentence.
The waiter filled the glasses with water.
Step 2: Break it into parts.
Subject is the waiter, verb is filled (simple past), object is the glasses, and with water is a modifier.
Step 3: Recall the passive rule.
The object becomes the new subject, and we use was or were plus the past participle, ending with by plus the old subject.
Step 4: Choose the auxiliary.
The glasses is plural, so we pick were, giving were filled.
Step 5: Build the sentence.
The glasses were filled with water by the waiter.
Step 6: Reject the others.
Option A lacks the auxiliary, C makes the waiter the one filled, and D wrongly uses were with the uncountable water, so option B is correct.
\[ \boxed{\text{B. The glasses were filled with water by the waiter.}} \]