The dynamics of benthic invertebrate communities in Muuga Bay was described in connection with large-scale dredging activities. The spatial extent and duration of the effects were assessed by multivariate analysis and spatial modelling. In general, dredging had moderate effects on benthic invertebrates both in space and time. Still, dredging resulted in an elevated biomass of bivalves, namely that of Macoma balthica. These bivalves were more impacted on flat bottoms compared to steep slopes.