Hyporheic flow transports fine particles into the riverbed, which can lead to clogging of the bed and in turn affect hyporheic flow and exchange processes. Field measurements and numerical simulations show the formation of a low-permeability layer (LPL) near the bed surface due to fine particle clogging, and consequently reduction of exchange fluxes between the bed and river water. A characteristic porosity (ε*) and time scale were derived to quantify the clogging process and effects on transport. Both the exchange flux and mean solute residence time were found to follow a power law relationship with ε*. For the normalised particle exchange flux, the exponent is close to unity, i.e., a linear relationship with ε*. The results also showed significant effects of the fine particle concentration, pressure difference, sediment collision efficiency and fine particle diameter on the bed clogging. Large values of these parameters led to intensified clogging, with the formation of different types of LPL.