We had similar issues here after having to do a lice treatment (3 lots of it). DD wouldn't sit in the bath for absolutely ages (ie months) and would scream whenever I washed her hair. I did lots of encouraging (can you show mummy and daddy how you can sit down etc) and with the hair lots of talking about the water not going in her eyes and being extra careful.

Slowly we got there, she loves baths and showers again now, but still freaks a bit if the water runs over her face. If she gets lice again, I'm just doing the lots of conditioner and comb them out method rather than the special treatments - too much effort!!