The hypotheses that (1) different seagrass morphologies may facilitate different nutrient uptake rates under similar hydrodynamic forcing and (2) this effect on nutrient uptake rates is spatially explicit, with the highest uptake rates at edges of patches, where currents and turbulence are highest, were examined under unidirectional flow conditions. Homogeneous patches (2 m long) of two seagrass species (Cymodocea nodosa and Zostera noltii) with contrasting shoot size and density were placed in a race track flume. 15NH4+ uptake and hydrodynamic properties along a gradient from outside to inside the patch were measured at a range of current velocities (0.05 to 0.3 m s-1). For each velocity we also determined the height and bending of the canopy. Water velocity affected the ammonium uptake rate of both species. The almost double uptake rates of C. nodosa shoots, compared to those of Z. noltii, were mainly attributed to a twofold difference in the within-canopy water flow (Qc, m3 s-1). Spatial patterns in canopy water flow were highly correlated with spatial patterns in NH4+ uptake, thereby explaining the 20% higher uptake rates at the leading edge of both canopies. The correlation between spatial patterns in canopy water flow and ammonium uptake rates underlines the role of canopy and patch configuration in determining the functioning of seagrass landscapes and their associated ecosystem services, such as nitrogen assimilation.