By testing a water sample to see if it contains the pathogen that causes cholera
Dr. Snow does take a sample of water from the well and look at it through his microscope, but he is not specifically looking for the cholera-causing bacterium, Vibrio cholerae. Why not? Because he doesn't know that it exists or what it looks like. In fact, it would be another 30 years before the nature and appearance of the pathogen become widely known.
Instead, he looks for any evidence that the water is not clean; in this, he is disappointed:
I found so little impurity in it of an organic nature, that I hesitated to come to a conclusion.
The only effective way Dr. Snow can investigate his suspicions about the source of the cholera outbreak is