I went thru this with my daughter. Its the "getting water in the eyes" that they hate so much. I got my daughter to tip her head back and place your hand on her forehead so the water cannot run into her eyes. Perhaps explain by getting her to try it on a doll, or you showing her on a doll. The other option is goggles. I know that sounds silly, but my kids were all poor swimmers until they discovered swimming goggles. Now they love it and spend lots of time with their faces submerged. Hope this makes some sense.
If all else fails just think to yourself that it is a phase and will not go on for ever.

MY NEPHEW WAS THE SAME WAY. THEN I WENT TO A WORKSHOP ON SENSORY ISSUES W/ CHILDREN. AFTER HEARING HOW SENSORY ISSUES CAN EFFECT US AND CHILDREN I HAD A DIFFERENT OUTLOOK ON THINGS. SOMETIMES THEY DON'T LIKE THE FEEL OF THE WATER ON THEIR HEADS OR YOU COULD BE RUBBING HER HEAD TOO LIGHTLY WHICH IS IRRITATING TO THEM OR TOO ROUGHLY. I DON'T KNOW BUT IT IS A THOUGHT.