My ovaries are noticeably larger and my period has been brown not red the past 2 cycles. What is causing this to happen?

Periods can differ. Not every period wil be the same for every women in every month. Variability is ok and expected. The quality of your bleeding such as color, or clots or duration, can change without any significant problems in your system. Reagrdign your ovaraies, it is hard to ascertain what "bigger" means and if that indicates anythgin medically. You can always visit your obgyn to help you with these question.