Mapping drought avoidance qualitative trait loci (QTLs) in the Bala x Azucena population has revealed a locus on chromosome 7 where the Azucena allele increases leaf rolling but reduces leaf drying. A cluster of four aquaporin genes OsPIP2;1, OsPIP2;4, OsPIP2;5, OsPIP2;9 co-locate with this QTL. The hypothesis that this gene cluster and the QTL are functionally related was tested, assuming that aquaporin would be linked to drought avoidance via an impact on root hydraulic conductance. Bioinformatic analysis reveals that Bala has relatively rare haplotypes for each of these genes that are associated with the aus subgroup of rice, and it shares these with the aus cultivar N22 which was one of the two parents in its breeding. A novel technique for assessing root hydraulic flow using osmotic swelling of roots was developed. When paired near isogenic lines for the QTL were grown in the same pot, allelic variation in root hydraulic flow and conductance was revealed using the osmotic method and a purpose-built two-plant pressure chamber. Notably, the allelic difference in hydraulic flow/conductance was only strongly evident when plants were droughted. RNAi lines with reduced expression of OsPIP2;1 were identified which had a commensurate reduction in root hydraulic flow and conductance. These studies confirm the role of OsPIP2:1 in root hydraulic flow in rice, and highlight the presence of aus-specific allelic variation that appears to impact root hydraulic conductance and drought avoidance in rice.