In Batman Begins, the villian just makes the drinking water toxic. With todays AI and Biotech, one can create a new bacteria or virus and cripple water supply of cities. I am sure a suitable trained AI can get more creative with such low cost attack vectors.

Nah. You can't just engineer some sort of pathogen which will survive water purification treatments, or grow and reproduce in pure water without any nutrients. Real life isn't like the movies.