The present study was carried out to determine the efficacy of root foraging and the physiological response of Vallisnaria natans grown in heterogeneous sediments. V. natans was cultivated in two homogeneous and two heterogeneous sediments. The results suggested that V. natans grown in heterogeneous sediments presented a significantly higher root proportion in its total biomass, exhibited root foraging, and grew well, as indicated by a total biomass, ramet number, and plant height very close to those of plants grown in nutrient-rich clay sediment. Moreover, the more sensitive physiological response of the roots than the stems or the leaves to sediment nutrients suggested that root foraging occurred, and the approached values between the two heterogeneous sediments and the homogeneous clay sediment indicated that V. natans could satisfy its nutrient requirements via root foraging. The results may be useful in the recovery of macrophytes that remodel part (rather than all) of the substrate and can potentially improve habitats that are unsuitable for plant growth.