The blue mussel, Mytilus edulis, is a foundation species with ecosystem engineering functions in the brackish, non-tidal Baltic Sea. In this study from the western Gulf of Finland, the relationship between the spatial patchiness of blue mussels and the diversity of associated macrofauna was examined across small scales (cm to meters) for the first time in subtidal habitats. It was demonstrated by geostatistical tools that blue mussel abundance and the diversity of associated macrofauna varied and interacted at two depths. Simultaneously, classic analyses (ANOVAs, correlations and multivariate techniques) detected neither relationships between the abundance of blue mussels and their associated macrofauna nor differences in the abundance of mussels or the diversity of associated macrofauna between depths. Using semivariograms, differences in spatial heterogeneity between depths emerged: patchiness at 5 m and random patterns at 8 m depth. Cross-semivariograms detected negative spatial co-variation between blue mussel abundance and diversity of macrofauna at 5 m, but positive and neutral spatial relationships at 8 m depth. Combining the approaches suggested that high dislodgment of mussels in shallow environments causes this pattern. Dislodgement effects may be compensated for by increased turnover of small mussels in patches within mussel beds, which would result in reduced habitat space to support a high diversity of associated macrofauna. On the basis of our results, it is suggested that patchiness of an ecosystem engineer is an ecological response, or result of a disturbance, and the effects of patchiness propagate to the associated macrofaunal community reducing the diversity of the latter.