Abstract Background and Aims Roots and rhizomes are crucial for the adaptation of clonal plants to soil water gradients. Oryza longistaminata, a rhizomatous wild rice, is of particular interest for perennial rice breeding owing to its resilience in abiotic stress conditions. Although root responses to soil flooding are well studied, rhizome responses to water gradients remain underexplored. We hypothesize that physiological integration of Oryza longistaminata mitigates heterogeneous water-deficit stress through interconnected rhizomes, and both roots and rhizomes respond to contrasting water conditions. Methods We investigated the physiological integration between mother plants and ramets, measuring key photosynthetic parameters (photosynthetic and transpiration rates and stomatal conductance) using an infrared gas analyser. Moreover, root and rhizome responses to three water regimes (flooding, well watered and water deficit) were examined by measuring radial water loss and apparent permeance to O2, along with histochemical and anatomical characterization. Key Results Our experiment highlights the role of physiological integration via interconnected rhizomes in mitigating water-deficit stress. Severing rhizome connections from mother plants or ramets exposed to water-deficit conditions led to significant decreases in key photosynthetic parameters, underscoring the importance of rhizome connections in bidirectional stress mitigation. Additionally, O. longistaminata rhizomes exhibited constitutive suberized and lignified apoplastic barriers, and such barriers were induced in roots in water stress. Anatomically, both rhizomes and roots respond in a similar manner to water gradients, showing smaller diameters in water-deficit conditions and larger diameters in flooding conditions. Conclusion Our findings indicate that physiological integration through interconnected rhizomes helps to alleviate water-deficit stress when either the mother plant or the ramet is experiencing water deficit, while the counterpart is in control conditions. Moreover, O. longistaminata can adapt to various soil water regimes by regulating anatomical and physiological traits of roots and rhizomes.