Fine sediment deposition in streambeds can reduce pore water fluxes and the overall rate of hyporheic exchange, producing deleterious effects on benthic and hyporheic ecological communities. To increase understanding of the factors that control the reduction of hyporheic exchange by fine sediment deposition, we conducted experiments in a laboratory flume to observe changes in the rates of solute exchange and kaolinite clay deposition as substantial amounts of kaolinite accumulated in the streambed. Two long-term experiments were conducted, with durations of 14 days and 29 days. Use of a laboratory flume system allowed steady stream flow conditions to be maintained throughout both experiments, and alternating injections of known quantities of kaolinite and a sodium chloride tracer were used to assess the effect of clay accumulation on hyporheic exchange directly. In the first experiment, there was no bed sediment transport and kaolinite deposition formed a highly clogged near-surface layer that greatly reduced hyporheic exchange. Application of a fundamental model for advective hyporheic exchange indicated that the effective permeability and porosity of the streambed decreased substantially during the course of the experiment. In the second experiment, the kaolinite was prepared with different surface properties to be more mobile, and the experiment was conducted with a small degree of bed sediment transport. As a result, no distinct clogged layer developed, and the rate of hyporheic exchange was found to remain approximately constant throughout the experiment (29 days). These results indicate that increasing fine sediment loads, e.g. those that occur from changes in land use, can have substantially different impacts on hyporheic exchange and associated ecological processes depending on the stream flow conditions, the rate and frequency of bed sediment transport, and the extent of interaction of the introduced fines with bed sediments. Copyright © 2004 John Wiley & Sons, Ltd.