First we walked for literally hours to find a decent spot, back then minecraft (or at least the map we seeded) didn't naturally spawn oceans of great depth, so it took a while to find something large enough and with at least "some depth" to it. But the spot we ended up deciding on was no way as deep as it needed to be... therefore I swam down in the middle of the ocean dug into the dirt at the bottom over the course of a few trips, then made an air gap, from there we dug a tunnel to the coast which was to be our initial entrance to what was just a small underground room 2 blocks high. From here we dug north, south, east and west 45 tiles each and then set about creating a disc shaped room still 2 blocks high, just under the sea bed. It was about at this point Seadee put together some very nice diagrams of each verticle slice of what each layer of the outer shell of the biodome would look like, so we could ensure we were digging perfect circles.
The next phase of development was strip mining downwards, where we had Core and many others expand the height of our room downwards by about 25 blocks. At this point we'd dug out aproximately 159,000 blocks (though my Math could be very wrong, (45x45)x1.314159 ?). It was long and grueling work and what dynamite could be scavenged was later used to speed up the process slightly.
We couldn't just knock out the ceiling, as it would've created more blocks of water to remove later... So we started to create a huge wall in the water above around the edge of where our biodome would surface, ... we'd hit fairly significant deposits of gravel previously, so that, combined with sand was used to drop into the water within our walled area to displace and remove the water. We often did this in sections, filling a chunk of water with gravel, digging it out again and moving a wall of gravel forward until we'd gone from one side of our walled section to the other. Once this was completed we knocked out the ceiling of our subterrainian lair - which by this point we'd filled with grass via our original 100+ block tunnel to the coast, as this was back in the day that the only way to create grass was to migrate it block by block from somewhere else over a long period of time. >.> Our grassy cave was often filled with livestock.
And then .... the biodome building commenced! We started off with a 10 block high wall of sand stone at the base and then began building our hemisphere dome on top of this using thousands of blocks of glass, made from sand that we'd dug from a few nearby and some not so nearby deserts and then lovingly furnaced. Suffice to say, this took a VERY very...very long time.
Once this was done, we had a Biodome, surrounded by a huge wall, in an ocean ... we needed to remove the wall, but due to the way water works in Minecraft doing so would not simply 'allow the water back' to flow over our dome. The water we'd worked hard to remove, now had to be placed back. We created a checker board of dirt and other materials at water level around the dome, leaving holes that we could then drop buckets of water into, meaning that every other block at water level above the dome would once again be water, and removing the checker board seperating them would allow those water blocks to merge to create a flat surface once again. ... I can't stress enough how tedious this was to do.
I've no doubt that the entire project consumed, destroyed or displaced more than 500,000 blocks ... probably closer to 1 million or more. And if you included the craft bucket powered hyper railroad that takes about 20 minutes to walk, where every rail requires multiple peices of iron and sticks you might easily double this number.