How to RescueEdit
In the room containing the switch used to make cement, there is a tunnel underwater. Swim inside and follow the path, avoiding the Shrimps and maybe picking up the Seeker Launcher and Gold Tokens along the way.
When you reach the end, there will be a switch next to the door you entered from. Press it, and the door will close and the water will be drained. Move the crate to reveal a Pet Yums can, but more importantly, position it under the gap at the top. Press the switch to open the door and flood the room again, and use the crate to climb up to the structure above where Isabella awaits.