Question

How is infrared spectroscopy used to identify the presence of organic compounds in water samples?

Answer 1

It's not.

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Picking the appropriate solvent is important so that we know that the peaks we see are from the compound we're analyzing. Water has an IR spectrum with strong peaks in areas where we don't want to see it.

All alcohols, amines, and carboxylic acids, among other similar functional groups, have peaks in the `3500~3000 "cm"^(-1)` range. Using water would defeat the purpose of identifying those types of compounds.

A much better solvent is carbon tetrachloride `("CCl"_4)`, which has a doublet IR peak at `795` and `762 "cm"^(-1)`, and not much else otherwise. That's why it's a good solvent---it doesn't significantly overlap with peaks found in organic compounds.

Some other good solvents are acetone, diethyl ether, etc.