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Clogging of streambeds due to clay deposition influences the stream‐subsurface exchange flux and thus directly modulates hyporheic ecological and biogeochemical processes. Clogging of sandy streambeds has previously been studied under losing and gaining flows and during streambed movement, but not when these two flow conditions coincided. We conducted flume experiments to quantify the combined effect of moving bedforms and losing or gaining flows on kaolinite deposition and streambed clogging. The experiments were conducted by adding pulses of kaolinite in a flume packed with sand under a stream water velocity of 25 cm/s. We measured the deposition rates, dynamics of hyporheic exchange flux (HEF) and vertical hydraulic conductivity (K_v), and the vertical distribution of kaolinite at the end of the experiments under two losing and two gaining flows (Darcy velocity of 10 and 20 cm/day …