The underwater sensors are sensors on Atlantis that are able scan beneath the surface of the city and into the depth of the ocean.
At some point between finding the mobile drilling platform and the landing on the frozen planet, three of the scanners suffered damage, presumably either in the flight from Lantea to New Lantea, the Battle of the Super-hive or landing on the frozen planet. As a result of the damage, Atlantis was unable to detect that it needed to deploy a defense mechanism to protect the underside of the city from ice. Doctor Radek Zelenka eventually identified the problem and had a team of scientists build replacements for the damaged scanners. Guided by Zelenka over radio, a team led by Major Evan Lorne performed the successful repair at which point Atlantis' ice defenses finally deployed. (SGA: "The Lost")