Along with Fernanda Viégas, he worked at the Cambridge location of IBM's Thomas J. Watson Research Center as part of the Visual Communication Lab, and created Many Eyes.

In April 2010, Wattenberg and Viégas started a new venture called Flowing Media, Inc., to focus on visualization aimed at consumers and mass audiences.

Early work in 1996-1997 ranged from service pieces, such as worksheets to guide financial decisions, to expository graphical narratives on subjects such as bond yield curves.

[8] Subsequently, Wattenberg started a research and development group at SmartMoney, which was responsible for interactive charts, graphs, and simulations, as well as a library of visualization components.

Outside of his work at Dow Jones, Wattenberg is known for interactive visualizations that have introduced mass audiences to data sets ranging from baby names[9] to museum collections at NASA[4] and the Smithsonian.

Their work with visualizations such as History Flow and Chromogram led to some of the earliest publications on the dynamics of Wikipedia, including the first scientific study of the repair of vandalism.

[11][12] Wattenberg is one of the founders of IBM's experimental Many Eyes web site, created in 2007[13] which seeks to make visualization technology accessible to the public.

In addition to broad uptake from individuals, the technology from Many Eyes has been used by nonprofits and news outlets such as the New York Times Visualization Lab.

For example, his Shape of Song series (1999–2002) depicted the form of musical compositions; this project exists online as well as in prints that have been exhibited in multiple venues.