Should I replace all of the water if it sat for 2 1/2 years?

[bwaynen]

This is my first time opening a pool and I just took the cover off. The pool is half full, water is clear but has dark stuff growing on the liner - worm shaped with light area surrounding each dark shape. I have a submersible sump pump that I used to drain the cover - should I do the same for the remaining water and jump in there and scrub everything? Thanks.