The elongating internode of the panicoid grass Setaria viridis is being used as a tool to investigate the molecular and physiological mechanisms involved in sugar storage and cell wall deposition during stem development in bioenergy feedstocks. The elongating internode grows from an intercalary meristem at its base, and progresses acropetally towards fully expanded mature cells which store sugars. Along this gradient there is also a transition from synthesis of predominantly primary cell walls through to thicker secondary cell wall deposition. A transcriptome of the S. viridis elongating internode has provided opportunity to identify genes that may be involved in sugar and biomass accumulation. Water flow is key to both biomass generation and sugar delivery. Aquaporins, a protein family that primarily functions as water channels, are integral to water flow and play important roles in solute transport processes in stem development. We analysed the elongating internode transcriptome and identified candidate aquaporins SvPIP2;1 and SvNIP2;2 that were highly expressed in internodal regions undergoing cell expansion and sugar accumulation, respectively. Functional characterisation of SvPIP2;1 and SvNIP2;2 in the heterologous system Xenopus laevis oocytes indicated both aquaporins have water channel activity with pH gating. SvPIP2;1 may function as a water channel in developing stems undergoing cell expansion, whereas SvNIP2;2 may have a role in retrieving water out of mature internodes after solutes are delivered for storage.