Aquaporins facilitate water transport across biomembranes in a manner dependent on osmotic pressure and water-potential gradient. The discovery of aquaporins has facilitated research on intracellular and whole-plant water transport at the molecular level. Aquaporins belong to a ubiquitous family of membrane intrinsic proteins (MIP). Plants have four subfamilies: plasma-membrane intrinsic protein (PIP), tonoplast intrinsic protein (TIP), nodulin 26-like intrinsic protein (NIP), and small basic intrinsic protein (SIP). Recent research has revealed a diversity of plant aquaporins, especially their physiological functions and intracellular localisation. A few PIP members have been reported to be involved in carbon dioxide permeability of cells. Newly identified transport substrates for NIP members of rice and Arabidopsis thaliana have been demonstrated to transport silicon and boron, respectively. Ammonia, glycerol, and hydrogen peroxide have been identified as substrates for plant aquaporins. The intracellular localisation of plant aquaporins is diverse; for example, SIP members are localised on the ER membrane. There has been much progress in the research on the functional regulation of water channel activity of PIP members including phosphorylation, formation of hetero-oligomer, and protonation of histidine residues under acidic condition. This review provides a broad overview of the range of potential aquaporins, which are now believed to participate in the transport of several small molecules in various membrane systems in model plants, crops, flowers and fruits.