Designated as a Special Area of Conservation (SAC) under the EU Habitats Directive, the Zwin nature reserve is considered as ecologically highly important. The coastal lagoon functions as a feeding habitat for fish, crustaceans and birds. Since macrobenthos is essential for intertidal ecosystem functioning as a food resource, it is essential that we gain insight in the distribution patterns of macrobenthic assemblages. Furthermore, since restoration measurements have been conducted in the Zwin nature reserve to restore a natural hydrodynamic regime and to prevent siltation processes from occurring, an understanding of the impact of management actions on macrobenthic communities is crucial. Univariate and multivariate analysis revealed that spatial distribution patterns are clearly related to environmental variables such as median grain size, mud content and organic matter, which can be considered as indicative for the hydrodynamic regime. Spatial and temporal variation analysis by means of univariate statistics, revealed a shift in species composition in highly impacted zones due to restoration measurements. A multivariate approach showed a significant relation of macrobenthic assemblages with environmental variables. However, a significant scatter and overlap in species distribution is less indicative for disturbance due to management actions. Then again, given a high enough amount of sample replicates to reduce within zone and within year variation, impact of monitoring actions could be better unravelled. Thus, spatial and temporal analysis could serve as an important tool for monitoring effects of restoration measurements.