Female RES will lay eggs even without a male being present (just like chickens). They will not be fertile so throw them away. If you haven't done so already, you need to provide a nesting area for your female RES to have access to when she needs to leave the water to lay her eggs. If she doesn't have a nesting area she may lay them in the water as a last resource. But even then she still may be retaining some since she knows they shouldn't be laid in the water. If she becomes egg-bound, the eggs could rupture and she may die.
Here's a great site on creating nesting areas:
http://www.tortoisetrust.org/articles/Nestsites.htm
What is her set-up like? How big is she (shell length from tip to tip not including curve)?