We demonstrate the fast transfer of suspended particles from the boundary layer into the upper strata (z < 4 cm) of permeable sediments with topography‐related interfacial water flows. The transport is driven by pressure gradients (▵ P ≤ 3 Pa) generated when bottom flows (u ≤ 10 cm s−1) are deflected by small surface structures (z < 3 cm) of hydrodynamical or biological origin. Acrylic pigment grains of 1‐ and 10‐µm diameter traced the intrusion of particulate matter into sandy sediment (k > 2 × 10−11 m2) incubated in a laboratory flume. Increased pressure up‐ and downstream of small mounds (z = 2.5 cm) drove water 5.5 cm into the core, carrying suspended particles (1 µm) to 2.2‐cm sediment depth within 10 h. Simultaneously, decreased pressure at the downstream slope of the protrusions drew pore fluid from deeper layers (z ≤ 10 cm) to the surface. In the sediment, friction reduced the velocity of the particulate tracers, resulting in size fractionation and layers of increased particle concentration. Ripple topography (0.8–2.8 cm high) enhanced interfacial particle (1 µm) flux by a factor 2.3 when compared to a level control core. The pathways of the particle and solute tracers below a sediment ripple are explained with a source‐sink model that describes the pore flow velocity field. Our results suggest that bedform‐induced interfacial flows are important for the uptake of particulate organic matter into permeable shelf sediments.