Thermal imaging cameras often do not work well underwater. It is because water blocks many infrared wavelengths, just as an opaque barrier blocks visible wavelengths. Just like we can't see through paint, an infrared sensor can't "see" through deep water because the waves it detects can't pass through water.
Water presents another challenging issue for thermal imaging cameras, which has to do with thermal conductivity and specific heat. Water has a much higher heat capacity than air, so it takes four times as much energy to raise or lower the temperature of the same volume by 1 degree.
This means that an object loses (or gains) its heat energy faster and over a shorter distance than water. Objects in water are therefore more difficult to thermally image than objects in air.