Even tipping the water out, there simply isn't the air flow you need to dry out the bottoms.
Low pH issues are compounded by extreme wetness.
River rock is unnecessary.
Repot, use a soil with plenty of perlite, and when you do, check to see how soggy it was in there! Trust me, my local grow buddy was using those too and almost lost her mothers- when she gave them to me for doctor services, they were sitting in an inch of water inside the pot.