The study of absorption lines in spectra of distant quasars offers a unique view of the physical properties of hydrogen and metals in the intergalactic medium and in high-redshift galaxies. In this talk, I will discuss the prospects of mapping inflows and outflows in distant galaxies with absorption line systems using predictions from hydrodynamical cosmological simulations of massive galaxies that are fed by extended streams of cold gas. I will also present first results from an ongoing observational program that led to the discovery of two pristine gas clouds at z=3.