External Nesting Boxes-How to waterproof

I pretty much did what everyone is suggesting. I took off the nest boxes, and cut the sides at an angle. Then I got a strip of the vinyl baseboard from Home Depot and nailed it right above the hinges.
 
I wrestled with this exact same issue. I wandered Home Depot looking for a solution and I found it. There is a rubber seal that is designed for the bottom of overhead garage doors. it's a long strip but if you look at the end it's in the shape of a horse shoe. it's much thicker than inner tube, flexible but rigid enough that it keeps it shape fairly well.

Take it out of the box and cut off a strip that will go from end to end on your hinge. Lay it out flat and you will notice a lip on both edges. you will want to keep one edge, you'll understand why in a moment, and carefully slice off the opposite edge with a straight edge and sharp razor knife.

Place the strip over the hinge opening so that the natural curve of the strip turns toward the nest. The remaining lip should go up and against the side of the coop. The cut edge will be facing down and lay on the nest cover.

Using short exterior decking screws, attach the flap to the side of the coop, but NOT into the nest lid. If you place each screw just under the rubber lip on the top edge it will press this lip tightly against the coop.

Now run a bead of exterior black silicone seal along the entire upper lip where it meets the coop and smooth it into place with a wet finger to make a tight seal.

voila, you are done. By leaving the bottom edge free it will slide freely as you open and close the nest lid. The remaining lip makes a great semi-rigid surface to caulk.

Mine has remained flexible and dry through 105 degree days down to about 12 degrees. It's been through one monsoon style rain and not a drop of moisture in the nest.

I'l try and shoot some pics if you're interested.
 
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I put the hinge between the back of the door and the rail. The hinge never gets wet and the door becomes a shelf when open. The roof has shingles and where
the roof meets the wall I put caulk and a board across.
 
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You could also just get one sheet of that roofing material, and extend the roof over it a bit. Though I guess if the rain is driving sideways real hard, it wouldn't matter much. It's why we decided to have ours at the back, and covered by the roof. So far, it's stood up well and stayed dry through a bunch of storms.
 
Maybe oversize the lid flap, cover the hinge with a strip of rubber inner tube, and give the lid more of a pitch to shed the dew. Might want to add some ventilation too to cool the interior of the coop and allow air circulation to dry out what gets in
 
Thank you sooooooo much for all of your input!!! On Saturday, we took off the nesting box lid and but new sides for the box that put the lid on an angle. This also made it, so that when it rains, the water hits the middle of the lid and the hinged area stays dry! But because we live in Florida where we regularly have tropical storms, We also used this awesome foamy sticky stuff that you use when you install new house windows. We put a strip of this behind where the hinged area is and it is dry as a whistle! I will post pics later so you can see what we did! I appreciate everyone's input!
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