AbstractSeagrasses are critical coastal habitats that provide numerous ecosystem services. The inherent patchiness within meadows exerts a significant influence on the flow‐vegetation interaction, which, in turn, affects the array of services provided by these environments. We present field observations of vegetation distribution and hydrodynamic measurements within and surrounding an approximately 2 m diameter gap (bare sediment) in a fragmented seagrass meadow. We show that variability in mean flows and turbulence is correlated with meadow structure at small (O (100 m)) and large (O (102 m)) spatial scales. Our observations reveal that bare gaps within seagrass meadows lead to faster flows and lower bed elevations. Despite slower flow speeds above the dense seagrass adjacent to the gap, the rates of dissipation of turbulent energy above the vegetation are typically around an order of magnitude larger than above the bare bed. Associated with this enhanced dissipation of turbulent energy, we observed a dominance of down‐deceleration events promoting fluid exchange and mixing and driving mass flux into the canopy. Analysis of directional variograms demonstrates that the major continuity axis within NDVI (normalized difference vegetation index) imagery (used as a proxy for vegetation biomass) coincides with the major axis of flow on both gap and meadow scales. Conversely, along the axis of minor flow variance, vegetation remains dense and exhibits greater uniformity. These findings indicate a feedback mechanism between seagrass meadow patchiness and spatial structure through flow modification, which may be beneficial for plant development.