Weber-Shirk graduated in 1985 from Goshen College with a B.A. in physics. He completed a Master's degree in 1987 in agricultural engineering and his Ph.D. in 1992 in environmental engineering, both at Cornell University. Weber-Shirk began teaching at Cornell in 1995.
As the director of AguaClara his research interest is to develop sustainable small-scale drinking water treatment technologies. Weber-Shirk is the manager of the Environmental Engineering Laboratory and is the author of numerous software applications used for data acquisition and instrument control.