Since this is low-pressure sealing, you can keep it pretty simple, and just use a face seal, or, potentially, a radial seal. The radial might be better to use as the o-ring will stay in the channel, whereas with a face seal, the o-ring could fall out if you open the enclosure while on the water.

Select the groove depth so that it allows about 25% compression of the o-ring when closed. Good practice is to chamfer the edges of the groove so that there’s less risk of damaging the o-ring when opening, closing, re-seating, etc.

If you do go for a radial seal on the aluminum base, be aware of the movement of the o-ring when opening and closing the seal, that it doesn’t get caught in the clearance between the aluminum and the polycarbonate (an extrusion gap).

The only alternative sealing arrangement to an o-ring that I can think of is a gasket, but I wouldn’t recommend that for your application here. Gaskets have to be seated correctly, and if you’re going to be opening the enclosure regularly, there’s a chance it won’t seat correctly each time.

Stick with the o-ring idea. Just be sure that whatever design you choose, that it fits a standard o-ring size that’s easily sourced. You don’t want to be stuck trying to replace it with a strange size in a few years’ time.