I would use some O-ring material in a shallow trough. Cut to fit, and join the ends with a tiny drop of CA.

I like the little rare earth magnets for fastening things down. I do find that I have to key and epoxy them so that they stay put over time. If in doubt, a little vaseline on the O-ring would not go amiss.

Another choice that may be even better, as mentioned by Dodgy Geezer, is to use silicone to make a gasket in place.

@roycv Thanks - I have been considering evergreen channel to make a trough, as you have described. The tube at the bottom is a great improvement.

@roycv Very long ago I made a sub out of wood - dynamic diver with a lot of lead weight in it. The hatch was just a wooden section which slotted into a rebate, and around the inside of the rebate I put a 1/8" seam of silicone rubber. Held down by a couple of bolts, that hatch never leaked for the whole life of the sub...

Many years ago I had to make a hatch on a deck of a yacht which would often have the deck exposed to the water and flooding over the hatch. I cut the deck and made a hatch with a coaming which slid into a ply-lined reverse coaming going downwards. This had a U shape at the lower edge like a trough which the new hatch dropped into. In the trough I placed very thin tubing, it was the kind that you could get then for bicycle wheel valves. This was given a thin coat of vaseline (petroleum jelly) and the hatch was clamped down onto it using scaled down deck sail winches.
It never let a drop of water in although frequently under water when on a tack as the yacht had a very low free-board.
A bit OTT but it did the job.
Roy

@IanTurk Try Blutac. Roll a thin tube of Blutac and apply it around the periphery of the hatch which should made larger than the hole cut in the deck. This will "stick" the hatch to the deck and make it watertight. The hatch can be "levered" off as required. The blutac is then rerolled again into a tube and restuck to the periphery of the hatch and pushed down on to the deck again. Its easy inexpensive and lasts for a very longtime

@jumpugly Thanks - yes tubing, great idea. I have a stash of rare earth magnets, that I knew would come in handy one day!

@IanTurk
Hey there Ian!
I used small 6mm rare earth magnets on added cross members spanning the hole in the hull, and some rubber tubing (not vinyl) on the underside of the hatch.
Or the reverse, so the tubing rides slightly underneath and along the cut lines in the deck where the hatch was. It's a bit ticklish, but totally doable.
😉👍