Aquaporins (AQPs) are involved in a variety of vital plant physiological processes, including water relations, development, stress responses and photosynthesis. Nicotiana tabacum (tobacco) has 84 AQP genes due to its recent hybridisation and allotetraploid genome. We functionally characterised a diverse subset of tobacco AQPs spanning the 3 largest AQP subfamilies, selecting nine isoforms from the PIPs, TIPs, and NIPs. Using high-throughput yeast-based functional assays, we determined AQP permeability to water, hydrogen peroxide (H2O2), boric acid (BA) and urea. For each AQP, subcellular localisations in planta were established using GFP translational fusions. From 3D protein homology modelling, we found that the monomeric pore shape/size, selectivity filter region and NPA motifs is insufficient to comprehensively predict their transport capabilities. PIPs had the narrowest pore diameter and were permeable to water, H2O2 and BA. The pore in TIPs was wider and more cylindrical in shape than for the PIPs. TIP1;1s was permeable to all four substrates tested, and is highly expressed in leaves and flowers, suggesting it functions in multiple roles. By contrast, NIP5;1t, with a larger pore size than the NtTIPs, is only expressed in young flowers and enhanced permeability only to BA. Its homolog in Arabidopsis (AtNIP5;1) has the same substrate specificity and functions as a boron channel.