I also have a 12" x 12" sea chests, but mine come up 10" above waterline so I can reach down into them to clear through hulls, etc. If you are within an inch or so of the waterline you can either inflate a lift bag under that side of the hull or put a 55 gallon drum on the other side of the boat and fill it with water, perhaps two. Here in the BVI lift bags are easy to borrow and a dive tank fills the size that you need, which would also seal off the intake.
I would look at extending the sea chest above your waterline so you can access the interior whenever you want. While I have a grate on the entrance to my intake side also and rarely get anything in a through hull, I have had a plastic bag get sucked against the grate when I had all of my AC cooling pumps running - of course at 0200 - and was thankful that I could just reach down and pull it through the grate. The grate is expanded aluminum with 1" x 1/2" diamond shaped openings.
Since I started putting copper strips in my strainers I've had zero barnacle growth in the intake sea chest. On the other side of the boat I have the same sized sea chest into which all of the exits are plumped; AC cooling, bilge pumps, etc. This side has neither grate and nor below waterline through hulls so no copper strips and there is barnacle growth in that chest.
When I built the sea chests I used 1" Lexan for the tops with a screw off 6" access ports in the center. I can see what is happening, monitor the sea life and they make great viewing ports for checking the bottom where we are anchoring.
Bob Phillips, Another Asylum
Tortola, BVI
Robert Phillips
Doyle Sailmakers BVI, Ltd.
bob@doylecaribbean.com
Mobile 284-541-2206
Office 284-494-2569