During the construction of a deep-water port (JadeWeserPort), bathymetry, sediment distribution, and macrofauna community structure were studied in the Inner Jade, a highly anthropogenically impacted tidal channel located in the southern North Sea. In order to assess the effects of additional disturbance by dredging activities, macrofaunal community compositions between 2002 (before the construction work had begun) and 2010 (during the final construction phase) were compared. The sand extraction for land reclamation and the redirection of the fairway changed the bathymetry markedly. While the old fairway in the centre of the study area remained mud dominated, a general increase in coarser sediments was detected in 2010. The dynamic nature of the study area in combination with the direct and indirect effects of dredging increased bathymetric heterogeneity [measured by singlebeam (2002) and multibeam (2010) echo-sounder]. In 2010, the macrofauna community structure roughly resembled the different categories of dredging activities. The most recently dredged northwestern area was inhabited by a community, which was different from the community in the regularly dredged old fairway. Both were different from the community in the northeastern, non-dredged area. In the southern area, and in the transition areas between the other three communities, a fourth community was found. A general increase of macrofaunal abundance and taxa number was observed in 2010, with the exception of the recently dredged area. The structure of the macrofauna community during the port construction phase seemed to be determined by secondary dispersal of the dominant taxa and recolonisation by highly mobile and opportunistic species.