Fine sediment exchange between a stream and the surrounding subsurface influences downstream contaminant transport and stream ecology. Fundamental models for this exchange were developed on the basis of (1) the hydraulics of bed form-driven advective pore water flow and (2) subsurface colloid transport processes. First, a model was developed to predict the advective flow induced in a sand bed by stream flow over bedforms. The resulting “pumping” exchange rate was calculated based on the streamflow conditions, bed form geometry, and bed depth. The pumping exchange of suspended sediment was then calculated by superimposing advective transport and particle settling in the bed and including the effect of physicochemical filtration by bed sediment. The filtration coefficient approach was used to predict the reduction in the concentration of transported particles. Both settling and filtration cause colloids to be trapped in stream beds, producing a higher net exchange rate relative to conservative solutes. When transported particles are completely trapped in a single pass through the bed, the exchange calculation is simplified because only the particle flux to the bed must be considered. In this case, the net exchange rate may be adequately represented by an effective piston velocity (flux/concentration) or loss rate to the bed in the advection-dispersion equation for the stream. Solute and colloid exchanges are predicted by the models without the use of fitting coefficients; only measurable hydraulic and particle parameters were used as model inputs. Simulations are presented which show the effect of stream parameters, settling, and filtration on net particle exchange. This fundamental approach to modeling stream-subsurface exchange potentially has great utility for understanding and predicting the transport and fate of reactive substances in streams.