Factory speakers often have a stiff plastic shield that sits above them to keep the rain water off. You may be able to buy something similar. You are not going to be able to stop the water coming in.

(list 6284, Mk1 S/N 00299 4GB blue [for sale]. Mk2 S/N 080000094 26GB blue)
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(list 6284, Mk1 S/N 00299 4GB blue [sold]. Mk2 S/N 080000094 20GB blue)