SUMMARY Soil water uptake by roots is a key component of plant water homeostasis contributing to plant growth and survival under ever‐changing environmental conditions. The water transport capacity of roots (root hydraulic conductivity; L p r ) is mostly contributed by finely regulated Plasma membrane Intrinsic Protein (PIP) aquaporins. In this study, we used natural variation of Arabidopsis for the identification of quantitative trait loci (QTLs) contributing to L p r . Using recombinant lines from a biparental cross (Cvi‐0 x Col‐0), we show that the gene encoding class 2 Sucrose‐Non‐Fermenting Protein kinase 2.4 (SnRK2.4) in Col‐0 contributes to >30% of L p r by enhancing aquaporin‐dependent water transport. At variance with the inactive and possibly unstable Cvi‐0 SnRK2.4 form, the Col‐0 form interacts with and phosphorylates the prototypal PIP2;1 aquaporin at Ser121 and stimulates its water transport activity upon coexpression in Xenopus oocytes and yeast cells. Activation of PIP2;1 by Col‐0 SnRK2.4 in yeast also requires its protein kinase activity and can be counteracted by clade A Protein Phosphatases 2C. SnRK2.4 shows all hallmarks to be part of core abscisic acid (ABA) signaling modules. Yet, long‐term (>3 h) inhibition of L p r by ABA possibly involves a SnRK2.4‐independent inhibition of PIP2;1. SnRK2.4 also promotes stomatal aperture and ABA‐induced inhibition of primary root growth. The study identifies a key component of L p r and sheds new light on the functional overlap and specificity of SnRK2.4 with respect to other ABA‐dependent or independent SnRK2s.