Oil was sprayed through an atomizer into an initial chamber, which gave the oil a charge. A droplet of oil would drip through a hole in the bottom of the chamber into a second chamber separated by two horizontal parallel plates. He could adjust the potential difference between the plates so that the electric force on the oil balanced out with the force of gravity acting on it (net force zero.) The mass of the droplet was found by finding the terminal velocity of the oil after shutting off the power supply. He could then determine charge by setting electric force equal to the force of gravity and solving for charge. He determined that the smallest charge measured was 1.6 x 10^-19 C and that all of the charges measured were multiples of this base charge. Thus elementary charge was determined.
The water droplet would have gradually evaporated, reducing its mass. This would make it difficult to suspend because he'd have to keep adjusting potential difference between the plates. Determining charge would be difficult because he couldn't be certain of the mass. He probably couldn't determine a precise terminal velocity of the droplet either because he couldn't be certain what position it fell from. The results would be skewed because the measurements were so imperfect.