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Previous modeling studies of hyporheic exchange induced by moving bedforms have used a moving reference frame, typically corresponding to an individual moving bedform. However, this approach is not suitable for simulating the exchange and accumulation of immobile fine particles beneath moving bedforms, which commonly occurs in sand‐bed streams, as both moving and stationary features must be considered. Here we present a novel simulation framework that may represent arbitrarily shaped, generally aperiodic mobile bedforms within a stationary reference frame. We combine this approach with particle tracking to successfully reproduce observations of clay deposition in sand beds, and the resulting development of a low‐conductivity layer near the scour zone. We find that increased bedform celerity and filtration both lead to a shallower depth of clay deposition and a more compact deposition layer …