When it comes to waterfall charts and d3 you have very few options.
1) Your are on your own, which means you are free to draw it how ever you want (which is pretty much the coolness of d3)
2) You use this repo https://github.com/sattybhens/waterfall which will give you a horizontal chart. Has a mix of ruby and coffescript
3) You use this plugin that resembles to what most jQuery users or Highcharts users are used to which is a config object that generates a chart. https://github.com/climboid/d3Waterfall
Currently it only supports vertical waterfall charts. Feel free to use and contribute.