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I have read that the pressure in a water barometer at the top of the water column is around 0.5 psi and at such low pressures water should boil at around ~26°C (Room temperature). [1] [2]

Water barometer
(source: thermospokenhere.com)

How come the water in the column near the surface doesn't boil?

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I believe that in the top you'll find it's the saturated vapor pressure of water.
http://en.wikipedia.org/wiki/Vapour_pressure_of_water (80 F ~27 C vapor pressure of about 27 mmHg or 27mm/760 mm * 14.7 = 0.52 psi.. not bad.

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Taking an intuitive guess here:

The pressure above the water column is indeed very low, and water molecules at the surface may escape - but they are also held back by the surface tension of the water (is your meniscus concave or convex?). There is an equilibrium here, and the temperature is low enough that the water won't boil off all at once. So at room temperature a water barometer can work "reasonably well" - for a while. Eventually the void fills with water vapor, and the water column will drop (as the pressure in the void rises). Eventually you get an equilibrium where the water vapor above the column reaches saturation for the given temperature.

The residual pressure of 0.5 psi is just about what you expect: it's the saturation point for water at 26 C, so the point where water vapor re-enters the liquid as fast as it escapes.

I conclude that you need to know the room temperature to make the appropriate correction to the pressure reading from the barometer - both for the density of the water, and more importantly to compensate for the vapor pressure in the void.

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