The intergalactic medium (IGM) accounts for ≳ 90% of baryons at all epochs and yet its three dimensional distribution in the cosmic web remains mostly unknown. This is so because the only feasible way to observe the bulk of the IGM is through intervening absorption line systems in the spectra of bright background sources, which limits its characterization to being one-dimensional. Still, an averaged three dimensional picture can be obtained by combining and cross-matching multiple one-dimensional IGM information with three-dimensional galaxy surveys. Here, we present our recent and current efforts to map and characterize the IGM in the cosmic web using galaxies as tracers of the underlying mass distribution. In particular, we summarize our results on: (i) IGM around star-forming and non-star-forming galaxies; (ii) IGM within and around galaxy voids; and (iii) IGM in intercluster filaments. With these datasets, we can directly test the modern paradigm of structure formation and evolution of baryonic matter in the Universe.