Aquaporins (AQP) are a family of membrane channels primarily responsible for conducting water across cellular membranes. The availability of a large body of high resolution structural data along with numerous atomic-scale simulation studies have resulted in an unprecedented level of understanding of the mechanism of function and selectivity in AQP. In this article, after summarizing major highlights of structure-functional studies of AQP, we will report on some of our recent large-scale molecular dynamics simulations investigating the mechanisms of permeation of various substances through pure lipid bilayers and through multiple pathways provided by tetrameric structures of different AQP. Comparison of the results obtained for structurally highly homologous, but functionally distinct, AQP allowed us to identify novel mechanisms of gating and selectivity of these channels and to design mutants with experimentally verified, altered properties. When applicable, special attention will be given to specific aromatic amino acids and their involvement in various functional aspects of AQP.