Contrasting emphasis of an uncountable noun

I didn't have any trouble figuring out that you were talking about a clepsydra. The antecedent to the word "one" has to be "device," since the other singular candidates "glass" and "metal" (as construction materials) aren't countable. This is nicely emphasized by "like" and "except"

I would drop the definite article in front of water: "water flows" instead of "the water flows." This is your definition, and you haven't established that water is the moving substance until the end of the sentence. After you have, you may say something like: "The user pours the water into the top vessel."

It is hard to contrast one item with another in this way unless a) we explicitly mention the original item that the new one is being contrasted with or, b), we use intonation. Unfortunately, there is no explicit intonation in writing unless we wish to use orthographic devices such as italics:

Like an hourglass, the device is made of glass and metal, except that in this one, water flows from one vessel into another.

The above should work perfectly well. However, we may well feel that the rampant use of italics is not very good style for our particular medium and opt for a different method. Another problem with trying to give contrastive emphasis to water in this sentence is that it occurs right at the beginning of a clause. There are a number of grammatical devices that we can use to help us here. One of the most useful is what is often known as an it-cleft (not to be confused with an extraposition). This is normally used as a focussing device. This construction makes the word or phrase being focussed on the head word of the complement phrase. This is then modified by a relative clause which details the further information. In the Original Posters case the larger clause would look like this:

• It is water which flows from one vessel to another.

If we reinsert this into the Original Poster's sentence we get:

Like an hourglass, the device is made of glass and metal, except that in this one, it is water which flows from one vessel into another.

This is one of the Original Poster's solutions. This construction does put the emphasis on the water and not so much on the flowing from one vessel to another. Part of the reason for this is that the flowing from one vessel to another is seen as already familiar information. It has the status of old (and therefore de-emphasised) information in the discourse.

Of course if you're happy to use italics, you could use an it-cleft and italics together:

Like an hourglass, the device is made of glass and metal, except that in this case, it is water which flows from one vessel into another.