You are truly in a theme park at Disneyland because every single line for every ride has something cool about it that makes you feel like you are somewhere else. The Jungle Cruise has lots of detailed information in pictures, posters and props throughout the line.
The water is murky that way on purpose, it's to hide the under the scenes action that guides the boats and directs the "dangerous" things that happen on this ride. The murky water keeps you from seeing all the stuff that controls everything on the ride. The water itself is about 5 feet deep, it's part of the Disneyland dark water system. This system of water travels through south from the north end of the Rivers of America in Frontierland and through Fantasyland, it wraps around the front of Sleeping Beauty's castle to create the moat. The water travels under the entrance of Adventureland by the Enchanted Tiki Room and runs through to the Jungle Cruise. It used to be 1,640 feet in length before being slightly shortened to build Indiana Jones in 1994.