I've been on Caribbean side of CR twice and never saw any muddy, dirty water. When it rains, there are many rivers that empty into Caribbean and it does get stirred up. Cocles Beach is a few miles south of Puerto Viejo. I am just the opposite, did not care for Pacific side of CR, but absolutely loved Fortuna, Tabacon Hot Springs and Arenal area.
Jane, I need to send you my pics so you and french chef BF can see what it looks like!