The bed morphology of dynamic surface water systems has always fascinated people, not only for safety reasons related to e.g floods and environmental disasters, but also for the wish to understand and predict the impacts of the ever increasing human interference with these systems. Understanding and predicting biogeomorphological processes, however, involves a wide range of disciplines such as hydrodynamics, hydrology, geology, chemistry, biology, ecology, oceanography and civil- & environmental engineering. If new insights need to be implemented, disciplines like social sciences, public administration, law and economy also come into play.

The improved understanding of biogeomorphological systems shows that their behaviour is governed by complex interactions between a number of physical and ecological processes and the morphological changes they cause. Yet, knowledge gaps remain due to the complexity of the processes and their interactions in natural systems. Successful application of (numerical) biogeomorphological models in realistic situations therefore requires expertise and a good overview of what is known and where the uncertainties are.

Driven by the increasing insight into the role of biota in geomorphology, the interdiscipline biogeomorphology is developing and biogeomorphological models are being set up which integrate hydrodynamic, morphological, water quality and ecological processes and their interactions at relevant scale levels. The model system described herein belongs to this category. For the time being, it focuses on coastal and estuarine applications.The biogeomorphological coastal modelling system has been validated against typical analytical solutions, flume experiments and a practical application (Ye, 2012). Furthermore, the system was tested in various practical applications, as described below. 

When using Delft3D-FLOW for the hydrodynamics, one can couple the Delft3D-WAQ module using the communication file from the flow model. The Delft3D-FLOW and Delft3D-WAQ models can be build separately, for instance in the associated graphical user interface (GUI). For online-coupling between Delft3D-FLOW and Delft3D-WAQ, first set up a flow model and tick the online-coupling box for WAQ. Furthermore, a coupling interval (indicated as the communication file interval) must be specified (see image). Activating the online coupling with Delft3D-WAQ initiates the WAQ-GUI upon execution of the flow model. This enables setting up the WAQ model like in a stand-alone or offline coupled case. Note that the specified coupling interval should be identical to- or a multiple of the communication file time interval.

More advanced options are available, for instance using keywords, etc. Here we refer to the various Delft3D manuals, for instance on the OSS-manual page page, as the entire biogeomorphological coastal modelling system is elaborately described in these manuals. The standard Delft3D release (trunk) contains a coupling program (with Delft3D-WAQ) for the biogeomorphological coastal modelling system. The bed state module, vegetation population dynamics module, sediment transport module and geomorphological bed updating module are part of the trunk Delft3D-WAQ release.

Delft3D is open source and can be obtained for free at the OSS-site. As of 01-01-2013, Delft3D-WAQ is open source as well, making the biogeomorphological coastal modelling system completely open source. The open-source version of Delft3D-WAQ is also available at the same location as the open-source version of Delft3D-FLOW. Currently, interested users can obtain a precompiled version of the entire Delft3D-suite (including FLOW, WAVE, WAQ, MOR, PART, etc.).

^{For Delft3D open-source users: the GUI can be be requested here.}

Relevant software

Delft3D:

• Source-code (OSS account required)
• Delft3D-Suite, a precompiled version of the entire Delft3D-suite (including FLOW, WAVE, WAQ, MOR, PART, etc.).
• D-Flow FM 

1. Lake Veluwe

For Lake Veluwe, a semi-enclosed lake between the old mainland and the Flevopolders in the Netherlands, spatially distributed measurements of the amount of macrophytes are available yearly from 1994 to 1999. This dataset was used to validate the ecological component of the model system. Figure 2 shows measured and computed Chara aspera population densities and distributions from year 1993 to 1997, indicated as population density classes from low (1) to high (7) (differences in initial conditions are due to data interpolation).

Although little effort was put into the model calibration, the observed spatial patterns of two macrophyte species in the lake are represented reasonably well by the model.

2. Schematized tidal basin

A schematized tidal inlet system was considered in relation to a salt marsh restoration project in San Francisco Bay - USA (schematized to make it more general). In Figure 3, the influence of saltmarsh formation on the morphological evolution is clearly visible: please note the modelled morphological evolution over time, with (center) and without (left) saltmarsh effects (z-level (m)). The vegetation distributions are shown in the right panels (from no vegetation (0%) to fully occupied (100%)). 
Qualitatively, this influence could be described as a decrease in channel depth, which are also more narrow. This is well related to physical reasoning (increase in critical shear stress near vegetation hampers channel evolution). Furthermore, it was found that sediment exchange (export for this specific case) through the tidal inlet decreased significantly (approx. 50%). For additional information, refer to Ye, 2012.

3. Salt marsh restoration in Nisqually estuary, Puget Sound, USA

In the Nisqually estuary a saltmarsh restoration project was executed in 2009. By removing a dike, an area of 308 ha was exposed to salt water. Soon after removal of the dike the existing freshwater vegetation died off, old channels reopened and grew further inland, flushing almost all dead vegetation. The biogeomorphological modelling system should be able to reproduce this scenario. Figure 4 shows the observed morphological changes in the first 7 months after the dike removal. Although the parameters of the ecological processes are far from perfect, spatial patterns of the vegetation distribution are reproduced, qualitatively. The effects of vegetation on morphology appears significant. An increase in sedimentation on tidal flats (where vegetation grows and spreads) is observed, furthermore, sedimentation in channels decreased. Unfortunately, due to a lack of measured data, only qualitative comparisons could be made. As an example of the modelled vegetation growth, Figure 5 is shown, which shows the modelled vegetation pattern (Phalaris arundinacea – reed canarygrass) after three years, which follows tidal channels as (qualitatively) observed (for initial conditions, refer to Ye (2012)).

For more information on these (and some additional) cases we refer to Ye (2012).

4. Impact of salt marshes on tidal channel(s) (formation)

A study by Schwarz et. al. (in prep. 2013) focusses on the initial development of saltmarsh channel networks in relation to vegetation. Not only was the influence of the presence of vegetation on tidal channel formation shown again, but also the influence of the vegetation characteristics (e.g. stiffness, stress tolerance, spatial expansion velocity, etc.) on morphological development. Figure 6 shows the channel network formation (after three years) for different vegetation species (Spartina alterniflora (cordgrass) and Scirpus mariqueter, both typical saltmarsh vegetation species)). The modelling results species comparison shows: (a) Initial plant cover (%); (b) Plant cover after 3 years (%); (c) Drainage basins and networks; (d) Cumulative sedimentation (pos.)/erosion (neg.) after 3 years (m); (e) Initial bed level (m); (f) Bed level after 3 years (m).

Finally, Schwarz et. al. (2012) concluded that the characteristics of existing channels, in relation to vegetation-flow interaction, strongly determine the nature of morphological changes (e.g. in tidal flats and channels).

• Schwarz, C., Ye, Q., van der Wal, D., Zhang, L., Ysebaert, T., Herman, M.J.P., 2013. 'Impacts of salt marsh plants on tidal channel initiation and inheritance' 
• Ye, Q., 2012. 'An approach towards generic coastal geomorphological modelling with applications', Delft University Institutional Repository