After having lowered the level of the water around the electric generator the walkthroughts say "dive into the water". How? The water level is too low and Indy gets killed as he falls!
make sure you land in the middle. If this doesn't work, try jumping to the platform.
There is two water levels, depending on which sercut you disconected. disconect the top one and the water drops down half way which will be even with a platform you can climb out of the water on. The bottom level of water is too shallow, thats what is getting him killed.