Obstructions that protruded from a laboratory test bed into the benthic boundary layer were exposed to gradients in longitudinal velocity (δu/δz) that produced vertical pressure gradients along the surface of the obstruction. These pressure gradients generated vertical secondary flows that may have ecological significance for benthic fauna and aquatic macrophytes. Laboratory experiments demonstrated that secondary flows of up to 15% of the local longitudinal velocity were produced behind individual obstructions within a submersed plant‐like or animal tube array and for conditions like those found in aquatic canopies or colonies. Our observations support theoretical predictions based on a reduced form of the Navier‐Stokes equations, confirming that the ascending flow is controlled by a local balance of vertical pressure gradient, proportional to δu2/δz, and viscous stress. The secondary flows were shown to transport dye from the bottom to a height dictated by the in‐canopy current speed and turbulence intensity. By extension, the ascending flows can potentially contribute to the advection of nutrients from sediments, where they have been regenerated by microbial processes, to areas higher in the canopy, where they can be used by epiphytes and macrophyte leaves. Pressure gradients generated near the stem base also produce pore‐water exfiltration. The coupled pressure‐driven exfiltration and vertical advection have the potential to control nutrient availability in the bed.