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The roughness height of the bed is one of the most important and difficult parameters to quantify in order to model the sediment dynamics.

In intertidal areas such as the Eastern Scheldt the bed roughness is not only influenced by abiotic factors (such as grain size, ripples and sand waves) but also by biotic factors (such as mussel beds, oyster reefs, diatom mats, lugworm fields and tube building worm fields) (Borsje, 2010). Diatom mats glue the sediment together and facilitate the deposition of fine sediment, resulting in a flat bed with a roughness height of several millimetres. Some biogenic structures like mussel reefs, oyster reefs and fields of tube building worms influence the roughness height directly. While other, such as lugworms, influence the roughness height indirectly. Lugworms excrete faecal matter on top of the sediment causing a topography of several centimetres.

The bed roughness tool, a mathematical model, can be a useful instrument for hydraulic engineers to quickly set up a bathymetry with a variable roughness of the surface. The roughness tool was used to reproduce the hydrodynamics based on both physical and biological processes. In a simple 2DH model including mussels showed a reduction of flow velocity by 27%, which is in agreement with field measurements.

    General Tool Description


    Sediment dynamics in the intertidal area are the result of the complex interaction between hydrodynamics and biological activity. Bed roughness is one of the most important and difficult parameters to quantify in order to model the hydrodynamics and sediment dynamics.  Bed roughness can be generated by physical characteristics (ripples, sediment grain size) and by benthic organisms that modify the surface.

    Either by stabilizing or destabilizing the sediment, biological activity is able to modify the sediment fluxes by a factor 2 and more, compared to the solely physical case (Graf and Rosenberg, 1997). The direct effect of biota on sediment dynamics is demonstrated in different field studies (e.g. Widdows and Brinsley 2002; Le Hir et al., 2007), laboratory flume studies (e.g. Friedrichs et al., 2000; Bobertz et al., 2009) and different model studies (e.g. Paarlberg et al. 2007; Borsje et al., 2008). Apart from the direct influence of sediment (de)stabilization by biota, also indirect effects by biota are known to influence the sediment dynamics. The most important indirect effect by benthos is added roughness by biogenic structures to the bed (Friedrichs and Graf, 2009). Given the recolonisation of benthos after an intervention, the roughness will also vary temporally. Moreover, many biological processes show a seasonal variation. Lugworms for example show a much higher biomass in autumn compared to late winter (Beukema, 1974) and microphytobenthos show a peak in April and July (Cadée and Hegeman, 2002.

    Tool description

    The roughness tool is a first step in the translation of biological and physical roughness elements into hydrodynamics and sediment transport. Five different roughness elements are defined: diatom mats, mussel beds, lugworm fields, tube building worm fields and sand ripples. All these roughness elements have typical roughness heights, and are important to predict the hydrodynamics and sediment dynamics correctly.

    Roughness element

    Roughness height k{}s* *[m]

    Diatom mats






    Tube building worms


    Sand ripples


    Default roughness (the rest of the surface)


    Based on the roughness elements defined by the user this tool has the capability of creating a roughness height map. This map can be used as input for a hydrodynamic model (e.g. Delft3D) to investigate the impact of spatial varying roughness heights caused by biological features on the water level, flow velocity and bed shear stress.

    How to Use


    The module is constructed in MATLAB. The output of the tool is a file type that can be imported in a hydrodynamic model, like Delft3D, to describe the roughness height in the different cells. It is recommended that users acquire a basic understanding of the implemented formulations prior to use.

    Input of the module

    • Bathymetry
    • Location of the roughness elements present in the area
    • Hydrodynamics

    After starting the module, a map with the bathymetry of the area is plotted. The map is restricted by a lower limit of -2 m NAP, which is the lower limit of the dry area during the ebb period. This limit can be adjusted to the specified area. Areas below this limit are filled dark blue.

    Next, the user is asked to manually click a polygon of the chosen roughness element onto the bathymetry map. The polygon is closed by clicking on the first node again (the cursor will change in a circle to close the polygon). After the first polygon is filled, all other roughness elements have to be defined in the same way. After defining the last roughness element (sand ripples) and overview map is given (adjacent figure). This overview shows in the left frame the bathymetry of the area (in this case the Galgeplaat) in m NAP and in the right frame the roughness height ks in m on the hydrodynamic grid.

    The output of the module is a .rgh file, which can be used in the hydrodynamic model (e.g. Delft3D) calculation to prescribe the roughness height at the different cells. The default roughness height (ks = 0.075) is used for the cells where no polygons are defined.

    Practical Applications


    Projects that can benefit from the tool are projects in which the biotic features are expected to have an impact on the roughness height. The tool is applicable in the Planning and Design Phase, to analyse the effects of different biological structures on the hydrodynamics and morphology.

    Results for the Galgeplaat

    In order to determine the relative impact of the different roughness elements on the Galgeplaat, the variable roughness elements are included in an existing hydrodynamic model set-up (Das, 2010).

    The model is run for just one day (1 November 2009), with realistic boundary conditions. Evaluation of the model results is done on the water level, flow velocity and bed shear stress. Moreover, evaluation of the model results is done on the time a certain value of the bed shear stress is exceeded. The bed shear stress is a measure for the sediment transport and gives insight in the possible impact of different roughness elements of sediment transport.

    As shown in adjacent figure the flow velocity is influenced by the difference in roughness height, resulting in a major impact on the bed shear stress. The time the bed shear stress exceeds 0.2 N/m2 is both increased and decreased by the roughness elements. Surprisingly, not only the bed shear stress is influenced at the location of the roughness elements, but also on a larger scale.

    For example, the diatom mats induce lower bed shear stresses, however due to the increase in flow velocity the bed shear stress outside the diatom mats is increased. The same explanation could be given for the tube building worms.

    In practice both diatoms mats and tube building worms patches show an elevation compared to the surrounding area, which could be caused by the active particle uptake by both bio-engineers, but might also partly be caused by the mechanism showed in this model result. In mussel beds, the increased bed shear stress (and turbulence) is adopted to increase the food supply of algea and to eliminate the faecal pellets. Increased bed shear stress is also favored by lugworms, while they could also eliminate their casts.


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