The aim of this study was to quantify the effect of bottom and suspended mussel cultures, cultured in different physical environments, on the sedimentary environmental conditions and thereby the biodiversity structure of the associated macrofaunal community. We compared two bottom cultures (Limfjorden: microtidal, wind-driven; Oosterschelde: macrotidal) and one suspended culture (Ria de Vigo in an upwelling coastal region). The sedimentary environmental conditions (mud fraction, POC, PON, phosphorus content, chl a breakdown products) were significantly elevated underneath and surrounding bottom and suspended cultures compared to culture-free sediments that were nearby and hydrodynamically similar. The relative change in environmental conditions was more pronounced in the Oosterschelde compared to Limfjorden, most likely due to differences in hydrodynamic forcing and characteristics of the mussel bed. The effect of the suspended cultures in Ria de Vigo on the surrounding sediments was influenced by local topographic and hydrodynamic conditions. The impact of mussels on the benthic community due to biodeposition was clearly seen in the community structure. The species composition changed from species which are typically present in sandy environments to more small opportunistic species, which are typically present in organically enriched sediments. The impact of bottom cultures on the benthic community due to changes in the habitat under the presence of mussels was positive, especially in the Oosterschelde where an increase in the number of epibenthic species was seen. The influence of bottom cultures on the sedimentary environment and on the macrobenthic community seems to be very local. Within the mussel site in Limfjorden, differences were detected between sites where none or almost no mussels were present with sites where mussels were very abundant.