Become Chicken-Clyde using one of the Dna combiners to either side of the ladders and fly up to the top.
You'll see a couple of gaps going up to a pair of levers. Pull each of them as many times as they'll produce rocks to seal of the drains belows. You'll need to pick up the ones from the right level as they'll land on the ledge and then drop them down the gap. Switch back to your frog clyde and you'll be able to swim down to the security machines.