This study investigates spatial patterns and temporal dynamics of aquifer–river exchange flow at a reach of the River Leith, UK. Observations of sub-channel vertical hydraulic gradients at the field site indicate the dominance of groundwater up-welling into the river and the absence of groundwater recharge from surface water. However, observed hydraulic heads do not provide information on potential surface water infiltration into the top 0–15 cm of the streambed as these depths are not covered by the existing experimental infrastructure. In order to evaluate whether surface water infiltration is likely to occur outside the ‘window of detection’, i.e. the shallow streambed, a numerical groundwater model is used to simulate hydrological exchanges between the aquifer and the river. Transient simulations of the successfully validated model (Nash and Sutcliff efficiency of 0·91) suggest that surface water infiltration is marginal and that the possibility of significant volumes of surface water infiltrating into non-monitored shallow streambed sediments can be excluded for the simulation period. Furthermore, the simulation results show that with increasing head differences between river and aquifer towards the end of the simulation period, the impact of streambed topography and hydraulic conductivity on spatial patterns of exchange flow rates decreases. A set of peak flow scenarios with altered groundwater-surface water head gradients is simulated in order to quantify the potential for surface water infiltration during characteristic winter flow conditions following the observation period. The results indicate that, particularly at the beginning of peak flow conditions, head gradients are likely to cause substantial increase in surface water infiltration into the streambed. The study highlights the potential for the improvement of process understanding of hyporheic exchange flow patterns at the stream reach scale by simulating aquifer-river exchange fluxes with a standard numerical groundwater model and a simple but robust model structure and parameterization. Copyright © 2011 John Wiley & Sons, Ltd.