A speaker and a microphone both need an opening to the air. A case that keeps water out has to put something over those openings, and sound passes through that layer less easily than through open air.
Researchers at the University of Texas at Dallas measured this with two iPhone 6s phones and a Samsung Galaxy S7 in a test box that generates and measures audio. Every phone put out less sound in a waterproof case than without one, and the team found cases could reduce speech recognition by as much as 50%. As lead researcher Linda Thibodeau put it, the plastic covering over the speaker reduced the sound getting out of the phone.
The researchers called their study limited, with a small sample, and said it shouldn't be generalized to other phone models. Treat 50% as a worst case from older phones, not a number for yours.
The same study found people with hearing loss are the most likely to be affected. Its suggestions: send call audio to hearing aids over Bluetooth, use the waterproof case only for activities like fishing, or text while the phone is cased.