Well, yes if the leads are insulated so the electrical connections do not come in contact with the water. The body of the thermistor is often coated with a waterproof substance or can be bought that way. I do not know of any reason that you can not use a thermistor to measure water temps.
Usually a thermowell - essentially a water proof tube - is used to prevent direct contact between the water and the sensing element. These are standard items that can be obtained from most temperature sensing suppliers.