The yellowing and dropping of leaves in the spring is normal for Southern Magnolia. Young trees often shed an excessive amount of foliage.
The browning of foliage is probably due to the standing water, which blocks oxygen from reaching the roots. Although Southern Magnolias can tolerate occasional flooding, as well as drought conditions, a young tree struggling to become established is probably less amenable to extreme conditions. If you have a thick layer of mulch over the roots, I would pull it back temporarily to allow the soil to dry more rapidly between downpours. Hopefully you will get a break in the weather soon.
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Here is a link that might be useful: Southern Magnolia
