Spatial patchiness of sediment characteristics in central, bathymetrically uniform sites in eight lakes was examined by comparison of within‐ and among‐core variation in water, organic matter, pigment, and phosphorus concentrations. Sampling sites were chosen to avoid known sources of sediment heterogeneity. Regression analysis of within‐core and among‐core variance on mean sediment characteristics was used to examine sampling exigencies. Comparisons of microscale and analytical variation with variation in sediment characteristics among core samples, within sites, showed significant (P < 0.05) sediment heterogeneity in >62% of the comparisons. All sediment characteristics and all sampling sites showed some significant heterogeneity. The variance in sediment characteristics among core samples, within sites, was from 2 to 320 times greater than analytical or microscale variation. Spatial heterogeneity might result from aggregated benthic animals, slow currents, or small‐scale variations in bottom profile.