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We used X‐ray difference microtomography (XDMT) and multi‐scale lattice Boltzmann (LB) simulations to investigate the deposition of colloidal particles in a streambed from the micron scale to the bedform scale. Flume experiments were performed to deposit zirconia colloids from suspension into a sediment bed composed of glass beads and covered with dune‐shaped bedforms. Following deposition, we extracted a series of cores over a single bedform, and analyzed the microstructure of colloid deposition patterns within these cores by XDMT. Colloids deposited primarily on the upstream sides of glass beads located at the upstream face of the bedform. Colloid deposits were also found in narrow pores and grain contacts, resulting from physical straining. We used the pore structure measured by XDMT as internal solid boundaries in pore‐scale LB simulations of pore water flow in order to define a constitutive …