I had horrible periods when I was her age, heavy bleeding, pain, etc. Since you didn't mention she has a lot of pain with this, I would suggest there is an imbalance somewhere. Sometimes kids just forget to eat and drink fluids when it's that time, and if she is bleeding a lot, she may need to eat more. I would definitely take her in and get a second opinion and get a full blood work up. Just to cover all the bases. It can tell if her electrolytes are low, or thyroid, or it could just be that she is just worn out. When you are an athlete, with a high metabolism, bleeding alot, and being 16 years old, that's stress enough. Been there, done that. Maybe just uping some vitamins or some extra veggies and fruit would help in the lunch, if she will eat them. Alternate, Gatorade and lots of water when she is working out. Keep lots of snacks handy too. I was a tall, skinny girl, but I could eat like a football player! HA!
Good luck! And just so you know I did have to go on the BC pill when I was 15 because it was the only thing that would keep me from staying home and throwing up from the pain. I know they have changed alot in the last 20 years, but it did help me out and I still knew all the dangers of having sex while being on the pill. You just have to have a good communication with her.