Start small, work on just leading her around the barn and arena and asking her to stop, and start, and turn calmly. Then lead her through a puddle or by obstacles till she obeys you quietly.
The KEY is for you to be the leader, the one she trusts. Don't loose your temper or yell, just be patient and keep asking. As soon as she even starts to to the right thing, praise her and release the pressure.
Do the same things while you are in the saddle. Keep your cool. My mare used to refuse to go forward, but she was perfect if I led her; anytime she would balk, I would just get off, lead her a little way, then get on again as if nothing had happened. She gave up the balking habit quickly. No fighting, no yelling, no whipping (tried that, didn't work.)
For water crossing, you may have to lead her across quite a few times, or have her follow another horse that she trusts. Don't loose your patience, you'll make the problem worse and longer to resolve.
Read John Lyons, he has exercises you can do to correct this problem.