The distinct turbulence dynamics and transport modulated by a common seagrass species were investigated experimentally using a flexible surrogate canopy in a refractive-index-matching environment that enabled full optical access. The surrogate seagrass replicated the dynamic behaviour and morphological properties of its natural counterpart. The flows studied were subcritical with Froude numbers $Fr<0.26$ and concerned five Reynolds numbers $Re\in [3.4\times 10^{4}, 1.1\times 10^{5}]$ and Cauchy numbers $Ca\in [120, 1200]$. Complementary rigid canopy experiments were also included to aid comparative insight. The flow was quantified in wall-normal planes in a developed region using high-frame-rate particle image velocimetry. Results show that the deflection and coordinated waving motion of the blades redistributed the Reynolds stresses above and below the canopy top. Critically, in-canopy turbulence associated with the seagrass lacked periodic stem wake vortex shedding present in the rigid canopy, yet the flexible canopy induced vortex shedding from the blade tips. Inspection of spatial and temporal characteristics of coherent flow structures using spectral proper orthogonal decomposition reveals that Kelvin–Helmholtz-type vortices are the dominant flow structures associated with the waving motion of the seagrass and that modulated the local flow exchange in both rigid and flexible canopies. A barrier-like effect produced by the blade deflections blocked large-scale turbulence transport, thereby reducing vortex penetration into the canopy. In addition, we uncovered a transition from sweep-dominated to ejection-dominated behaviour in the surrogate seagrass. We hypothesise that the vortices created during the upward blade motion period play a major role in the sweep-to-ejection-dominated transition. Conditionally averaged quadrant analysis on the downward and upward blade motion supports this contention.