Mercury manometers are very useful and reliable for measuring low absolute pressures. I use them regularly. These days most engineers have no idea what they are or how to even read one. Because of this they also have a rather poor understanding of the distinction between gage pressure and absolute pressure. The toxicity of metallic mercury (quicksilver)is extremely exaggerated. It is almost impossible to be absorbed by the body, even when swallowed. that is why we didn't all die, or even get sick as kids. Mercury in the environment from fluorescent lamps and coal power plants is more of a problem.
Water manometers are only used for measuring small differential pressures. Water has a very high vapor pressure and will boil under vacuum. There are low vapor pressure oils that can be used but the low density means the gage will be tall.