I don't know about special procedures for laying out a cal course underwater, but Bob Letson and I checked the length of a calibration course in Korea once during a pouring rain, when the standing water was up to curb height on top of the course. I can't remember what we used for intermediate markings-- clearly the masking tape method was out of the question-- other than that everything was the same, and we used a thermometer immersed in the water to assess the expansion of steel. Of course we were lucky that the water was just a few inches deep, no snorkeling needed.
The calibration course checked out. After that I remember hours of toweling off the tape so it wouldn't rust, while Bob told stories of measuring in the early days under Ted Corbitt's guidance.
We were there, we thought, to check the measurements for the Olympic marathon to be held in Seoul the following summer. That check never happened, but that's a whole other story.