Managing intertidal mud flats requires a knowledge about the physical and biological structure of these systems, their physical and ecological roles and the development and influence of socio-economic activities on these systems. In this paper it is shown how, against the background of the strong natural variation, the effects of dredging and anthropogenic eutrophication can be simplified, represented and applied for management purposes. Freshwater (nutrient) discharges differently but linearly affect the annual primary production in the three (Lower, Middle and Dollard) estuarine reaches. The differences in effect along the estuarine axis are primarily caused by the turbidity gradient. Channel dredging affects the slope of the logarithmic turbidity gradient between the turbidity maximum with relatively stable concentrations in suspended matter, and the North Sea near the barrier islands. The direct consequence of a varying slope of the gradient is that the most seaward situated reaches of the estuarine system are more strongly influenced by channel dredging than the upstream reaches. The relative effects of both channel dredging and eutrophication become more manifest in the lower reaches of the estuary than in the upstream parts. Based on the correlations found, the expectation is that mean annual river discharges lower than ca. 35 m 3 s −1 will turn the entire estuarine system to full heterotrophy. Results from experiments studying stabilization and destabilization by organisms are helpful to conceptual development, but are not helpful to any decision maker because the spatial scale of these systems usually does not fit the needs of an environmental manager who usually has to consider entire systems. Considering the aspect of scales results in the conclusion that at the process level (primary production process) the time scale in the Ems estuary is mainly determined by the seasonal cycle and much less by factors like wind and tide. From the management perspective and considering seasonality, the longer term effects of both anthropogenic eutrophication and channel dredging can be best judged based on an annual time scale. Weather conditions and human activities both impact either large parts of the estuary (wind resuspension, eutrophication) or the entire area (dredging), something that is due to the long tidal travelling distance in comparison to the length of the estuary. This results in the necessity to consider large areas when judging the environmental impact of the above-mentioned parameters. The available information about the socio-economic subsystem and the natural subsystem can be integrated in instruments like management knowledge systems or decision support systems to help us to structure discussions in prioritizing between policy options.