Gas phase during water sampling
That's a tricky question.

Given your setup, it follows that you will only be sampling water (not simply "fluid", mind you; fluid is a common term for both gas and liquid). But gases might be more or less soluble in liquids. Chances are that your water is saturated with some gas (say, $\ce{CO2}$) and pressurized with the same gas in the pure form. Then, as soon as you take your sample and put it in a sealed (or worse yet, unsealed) container, it will release some gas, and so the composition of the sample will become different from that of the liquid in the pipe.

Whether or not this issue is relevant to your situation, is up to you to assess.