Abstract Black reduced sediment surfaces (Black Spots) in sandy intertidal flats of the German Wadden Sea (southern North Sea) are characterised by elevated sulphide concentrations (up to 20 mM) and low redox potentials. It is assumed that the appearance of Black Spots is linked to elevated levels of organic matter content within the sediments. In order to establish the effect of high substrate and sulphide concentrations on the heterotrophic microbial communities in Black Spot sediments, bacterial abundances and the potential C-source utilisation patterns of microbial communities were compared in natural and artificially induced Black Spots and unaffected control sites. Bacterial numbers were estimated by direct counts and the most probable number technique for different physiological groups, while patterns of C-substrate utilisation of entire aerobic microbial communities were assessed using the Biolog sole-carbon-source-catabolism assay. Bacterial abundances at Black Spot sites were increased, with increases in mean cell numbers, more disperse data distributions and more extreme values. Substrate utilisation patterns of aerobic microbial communities were significantly different in Black Spot sediment slurries, showing diminished richness (number of C-sources catabolised) and substrate diversity (Shannon diversity index) in comparison to unaffected sites. Principal component analysis clearly discriminated Black Spot utilisation patterns from controls and indicated that microbial communities in individual Black Spot sites are functionally diverse and differ from communities in oxidised surface sediments and reduced subsurface sediments at control sites. This work suggests that potentially negative effects on microbial communities in Black Spot sediments, through anoxia and high sulphide concentrations, are balanced by the stimulating influence of substrate availability, leading to comparable or higher bacterial numbers, but lower functional microbial diversity of aerobic microbial communities.