Confirm the probe can enter water
Check the manual for liquid use, immersion depth and water-resistance. A waterproof probe does not mean its display or cable connector can be submerged.
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Guide
Usually yes for the metal sensing probe, provided the manual allows liquid use. Keep the display, connector and any non-waterproof joint above the water.

Check the manual for liquid use, immersion depth and water-resistance. A waterproof probe does not mean its display or cable connector can be submerged.
The temperature sensor may extend beyond the pointed tip. Cover the stated sensing zone while keeping prohibited parts dry.
Suspend it in the water without touching the bottom or sides. Contact with heated metal or glass can distort the result.
Water can form warmer and cooler layers. Gentle stirring evens the temperature; then wait until the display stops changing significantly.
Protect your hands from steam, do not lean over the vessel and account for altitude if using boiling water as an accuracy reference.
Common questions
It may measure the water if liquid use and the range are allowed, but keep non-waterproof parts dry. A purpose-built bath thermometer is easier and safer around children.
Only if the manufacturer explicitly labels the whole device waterproof to the required depth. Otherwise immerse only the approved probe section.
The vessel may be hotter or cooler than the surrounding water, so contact can bias the reading. Hold the sensing area away from surfaces.
Many suitable probes can be checked with a properly prepared ice-water slurry. Follow the manual; boiling-point checks require an altitude adjustment.