Seepage rate and direction measured with a seepage metre modified for use in flowing water were greatly variable along a 300-m reach of a shallow, gravel-bed river and depended primarily on the local-scale bed topography. The median value of seepage measured at 24 locations was 24 cm/day, but seepage measured at specific sites ranged from -340 to +237 cm/day. Seepage also varied substantially over periods of hours to days and occasionally reversed direction in response to evolution of the sediment bed. Vertical hydraulic conductivity was related to seepage direction and was larger during upward seepage than during downward seepage; with differences ranging from 4 to 40% in areas of active sediment transport to more than an order of magnitude in areas where current was too slow to mobilize bed sediment. Seepage was poorly related to hydraulic gradient measured over vertical distances of 0.3 m and appeared to be opposite the hydraulic gradient at 18% of the locations where both parameters were measured. Results demonstrate the scale dependence of these measurements in coarse-grained hyporheic settings and indicate that hydraulic gradients should be determined over a much shorter vertical increment if used to indicate exchange across the sediment-water interface. Published in 2009 by John Wiley & Sons, Ltd.