Main conclusion The regulation of source-to-sink sucrose transport is associated with AtSUC and AtSWEET sucrose transporters’ gene expression changes in plants grown hydroponically under different physiological conditions. Source-to-sink transport of sucrose is one of the major determinants of plant growth. Whole-plant carbohydrates’ partitioning requires the specific activity of membrane sugar transporters. In Arabidopsis thaliana plants, two families of transporters are involved in sucrose transport: AtSUCs and AtSWEETs. This study is focused on the comparison of sucrose transporter gene expression, soluble sugar and starch levels and long distance sucrose transport, in leaves and sink organs (mainly roots) in different physiological conditions (along the plant life cycle, during a diel cycle, and during an osmotic stress) in plants grown hydroponically. In leaves, the AtSUC2, AtSWEET11, and 12 genes known to be involved in phloem loading were highly expressed when sucrose export was high and reduced during osmotic stress. In roots, AtSUC1 was highly expressed and its expression profile in the different conditions tested suggests that it may play a role in sucrose unloading in roots and in root growth. The SWEET transporter genes AtSWEET12, 13, and 15 were found expressed in all organs at all stages studied, while differential expression was noticed for AtSWEET14 in roots, stems, and siliques and AtSWEET9, 10 expressions were only detected in stems and siliques. A role for these transporters in carbohydrate partitioning in different source–sink status is proposed, with a specific attention on carbon demand in roots. During development, despite trophic competition with others sinks, roots remained a significant sink, but during osmotic stress, the amount of translocated [U-14C]-sucrose decreased for rosettes and roots. Altogether, these results suggest that source–sink relationship may be linked with the regulation of sucrose transporter gene expression.Electronic supplementary materialThe online version of this article (10.1007/s00425-017-2807-4) contains supplementary material, which is available to authorized users.