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Abstract We utilized 251 measurements from a recently developed automated seepage meter (ASM) in streambeds in the Nebraska Sand Hills, USA to investigate the small‐scale spatial variability of groundwater seepage flux (q) and the ability of the ASM to estimate mean q at larger scales. Small‐scale spatial variability of q was analyzed in five dense arrays, each covering an area of 13.5–28.0 m²(169 total point measurements). Streambed vertical hydraulic conductivity (K) was also measured. Results provided: (a) high‐resolution contour plots of q and K, (b) anisotropic semi‐variograms demonstrating greater correlation scales of q and K along the stream length than across the stream width, and (c) the number of rows of points (perpendicular to streamflow) needed to represent the groundwater flux of areas up to 28.0 m². The findings suggest that representative streambed measurements are best conducted perpendicular to streamflow to accommodate larger seepage flux heterogeneity in this direction and minimize sampling redundancy. To investigate the ASM's ability to produce accurate mean q at larger scales, seepage meters were deployed in four stream reaches (170–890 m), arranged in three to six transects (three to eight points each) per reach across the channel. In each reach, the mean seepage flux from ASMs was compared to the seepage flux from bromide tracer dilution. Agreement between the two methods indicates the viability of a modest number of seepage meter measurements to determine the overall groundwater flux to the stream and can guide sampling for solutes and environmental tracers.