Putting surface water into an aquifer would be a natural disaster and would actualy contaminate the ground water.

Aquaifer water is naturally purified as water moves down through the ground. You can drink it without treatment. (most of the time).

Now, if we used large, underground caverns to store flood water for future treatment, that would be something. But flood water is full of bacteria, and unfortunately a lot of man made shit like plastic, heavy metals and chemics which can't be easily filter or separated by conventional water treatment.