Picking up batteries in Water Hazard
OK. I am going to answer this question simply because a few of you upvoted it for some reason (all three of you).
Just to be clear on the exact spot: after getting the gun added to the airboat in Water Hazard, you exit the camp and into the outdoors, escape the ambush in the canal lock, round a corner, and go through the long tunnel mentioned in the original question, until you get to a dry area. This will also be the very first load point after getting the gun added to the airboat.
There are a few options here, none of them very good:
Flail around helplessly in the water
This entire tunnel is surrounded by hazardous material in the water, and after exiting the airboat, it is difficult to jump up and use it as a step. But you can do it. Here's how: earlier in the tunnel, before you get to the dry area and the load point, back up against the walkway on the left and hop out. Flail around in the poisonous water until you somehow manage to lurch up onto the walkway. Now run all the way to the end of the tunnel, grab the batteries, and run all the way back to where you left the airboat sitting. There! You didn't have to go through the load point! (Are you happy now?)
Walk through the load point a few times
There is some good news here: once you get to the dry area, you don't need to use the airboat as a step at all. Just hop up on the walkway, go back a few steps, grab the batteries, and back a few steps to the airboat. You're done!
Yes, the load point is in an awkward spot if you want to go back for these batteries. It is placed exactly at the edge of the dry area, so if you want to use the dry area in any way, you must go back through the load point.
On a somewhat related note, just before this long tunnel with the batteries, you can use this same technique of jumping up on the airboat to get where you are not really supposed to go. During the ambush in the canal lock area, you are supposed to run roughshod over the CP units on the walkway on the right. But if you back up against the walkway on the left and hop out, you can jump up on the airboat and gain access to the secret CP bunker! (And there is nothing there!) Even better, you can charge up the higher walkway and try to jump over the top of the canal lock, only to be stopped by an invisible wall halfway up the ramp! Simply stunning!