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Quantitative acoustic marine habitat mapping needs to consider the impact of macrobenthic organisms on backscatter data. However, the sensitivity of hydroacoustic systems to epibenthic life is poorly constrained. This study explores the impact of a benthic community with sparse abundance on seafloor microroughness and acoustic backscatter at a sandy seafloor in the German North Sea. A multibeam echo sounder survey was ground-truthed by lander measurements combining a laser line scanner with sub-mm resolution and broad-band acoustic transducers. Biotic and abiotic features and spatial roughness parameters were determined by the laser line scanner. At the same locations, acoustic backscatter was measured and compared with an acoustic scatter model utilizing the small-roughness perturbation approximation. Results of the lander experiments show that a coverage with epibenthic features of 1.6% increases seafloor roughness at spatial wavelengths between 0.005−0.03 m, increasing both spectral slope and intercept. Despite the fact that a strong impact on backscatter was predicted by the acoustic model based on measured roughness parameters, only a minor (1.1 dB) change of backscatter was actually observed during both the lander experiments and the ship-based acoustic survey. The results of this study indicate that benthic coverage of less than 1.6% is insufficient to be detected by current acoustic remote sensing.