Heya,
I've done dry bags, pelican cases, ammo cases, lunch box, open carry, in a bag, you name it. If you want rapid access, lunch box, ammo box or dry bag is it, riding between your knees with a harness to keep it from going overboard. If you want maximum protection, pelican/apache case, and it might as well be strapped down and you don't access it unless you're off the boat.
Dry bag between the knees...
IMAGE LINK: https://flic.kr/p/s4FEsH 
IMG_7478 by
Martin Wise, on Flickr
Lunch box between the knees...
IMAGE LINK: https://flic.kr/p/yE6NqT CRW_0390 by
Martin Wise, on Flickr
Ammo box between the knees...
IMAGE LINK: https://flic.kr/p/TyzzQd IMG_0490 by
Martin Wise, on Flickr
IMAGE LINK: https://flic.kr/p/U5zKko IMG_0417 by
Martin Wise, on Flickr
Pelican case strapped in, access only if you're off the boat...
IMAGE LINK: https://flic.kr/p/svrkzN IMG_7739 by
Martin Wise, on Flickr
IMAGE LINK: https://flic.kr/p/ymK55u IMG_8485 by
Martin Wise, on Flickr
Overall I prefer the ammo box approach as it opens rapidly, but seals with a rubber gasket so splashes don't go in. Inside you can pad it.
You can see what I do. I'm not a particularly careful person on the water, I'm just experienced with it. And I've yet to dunk one nor take any real splashes that matter. My prime location for kayaking and shooting is in the tidal salt flats of the Gulf of Mexico where I photograph, fish and generally explore. I generally run with weather resistant gear for obvious reasons, but it hasn't mattered. So mostly 1D and 7D bodies. I take my phone and little cameras like the EOS-M or Hero along too. My telephotos are generally short fast L's. But honestly they don't seal against a dunk, and you wouldn't want a salt splash either. So really, weather resistant on a boat isn't much protection. Mist and spray are about the only thing you will protect against. Anything more is of course catastrophic for equipment.
Very best,
