Brain i'm assuming that sub enclosure is a premade box of MDF? If so in that position you can get water, especially coming over the bow and if it hits that MDF it'll swell and crumble so fast you won't believe it! Being as you can't see it i would recommend you pull it, strip that carpet and coat it twice with resin or spray on truck bed liner.

You can always put the carpet back on if you wish. I'm just saying ... seen it happen more than once!