During the construction of a deep-water port (JadeWeserPort), bathymetry, sediment distribution, and macrofauna community structure were studied in the Inner Jade, a tidal channel located in the southern North Sea. The relationships between macrofauna community structure and natural as well as anthropogenic environmental variables were investigated in this very heterogeneous study area. The manual expert hydroacoustic classification of the backscatter image derived by side scan sonar was successful to detect the different dredging activities and the natural bedforms in the undisturbed areas. The sediment distribution was very patchy and no significant congruence with the hydroacoustic classification could be identified. In contrast, low, but significant relationships between the hydroacoustic classification and the macrofauna community structure as well as the sediment distribution and the macrofauna communities were found. The most important impact on the spatial community structure was the number of days after the last dredging/dumping activity for the JadeWeserPort (JWP), followed by the sediment characteristics explained by grey values of the backscatter image. This study stresses the problems of benthic habitat mapping in such a heterogeneous area. In order to assess the effects of physical 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 navigation channel changed the bathymetry markedly. While the old navigation channel in the centre of the study area remained mud dominated, a general increase in coarse sediments was detected in 2010. The dynamic nature of the study area in combination with the direct and indirect effects of dredging increased the 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. A general increase in 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. The effects of the presence of two adult bivalve species with different feeding modes on the post-settlement dispersal of their juveniles were examined in a flume experiment
