Step 1: Read the active sentence.
The waiter filled the glasses with water.
Step 2: Pick out the parts.
Subject is the waiter, verb is filled (simple past), and object is the glasses, with the phrase with water added.
Step 3: Recall the passive rule.
In the passive, the object moves to the front and we use was or were plus the past participle.
Step 4: Choose the auxiliary.
The new subject the glasses is plural, so we need were, giving were filled.
Step 5: Build the full sentence.
The glasses were filled with water by the waiter.
Step 6: Reject the others.
Option A drops the auxiliary, C makes the waiter the receiver, and D wrongly uses were with the uncountable water, so option B is correct.
\[ \boxed{\text{B. The glasses were filled with water by the waiter.}} \]