Shoot the gas bottles from a safe distance. When they blow, they will provide access to the storage area.

After shooting the escaped "Lopers" (Does that sound like dutch for 'runners'?), one is still locked up. Find a very, very efficient weapon and waste the last one. Or prepare to get fried yourself. Then break the back wall of the containment cell, to get access to a secret.

Secrets 3 and 4 are connected: it is necessary to solve #3 to reach #4.
Jump into the well and swim to the grate behind the pipes. Break the grate. Swim through, find a valve and turn the handle.

After #3 is done, the area under a locked room with goodies have been flooded. Jump in, swim into the tunnel and up into the 'secret' room.