We conducted a series of tracer test experiments in 12 outdoor semi-natural flumes to assess the effects of variable flow conditions and sand addition on hyporheic zone conditions in gravel beds, mimicking conditions in headwater streams under sediment pressure. Two tracer methods were applied in each experiment: 2–5 tracer-pulse tests were conducted in all flumes and pulses were monitored at three distances downstream of the flume inlet (0 m, 5 m and 10 m, at bed surface), and in pipes installed into the gravel bed at 5 m and 10 m distances. The tracer breakthrough curves (total of 120 tracer injections) were then analysed with a one-dimensional solute transport model (OTIS) and compared with data from the gravel pipes in point-dilution pulse tests. Sand addition had a strong negative effect on horizontal fluxes (qh), whereas the fraction of the median travel time due to transient storage (F200) was determined more by flow conditions. These results suggest that even small additions of sand can modify the hyporheic zone exchange in gravel beds, thus making headwater streams with low sediment transport capacity particularly vulnerable to sediments transported into the stream from catchment land use activities.