You need to roof over your wished “area” and fill it with blocks (this will stop the water). After this, you can remove all unnecessary blocks. This may take a lot of reruns. Finished.
Light blocks are good for this, as Heurazic has said, because they break down extremely fast. I’ve dabbled in some under water building myself and found that you have to fill an area in; then hollow it out. Otherwise you’ll run into a mysterious issue of blocks leaking randomly between the cracks.