Presentation by Sarah Dzimballa (University Twente, Netherlands) at the Delft3D User Days, during the Delft Software Days - Edition 2023 (DSD-INT 2023). Thursday, 16 November 2023, Delft.

1. Process-based modeling of salt marsh
development coupling Delft3D FM with
a vegetation module in NBSDynamics
Sarah Dzimballa
Delft3D User Days –Water Quality & Ecology
16/11/2023

2. Coastal Ecosystems
2
Photo: S. Dzimballa
Salt Marshes Mangroves Coral reefs
Photo: S. Dzimballa

3. 3
Coastal protection
mudflat tidal marsh dike
Flood Protection
Photo: S. Dzimballa
Salt Marshes Characteristics

4. 4
Biogeomorphology
Hydrodynamics
• Tides
• Waves
Sediment transport
• Sedimentation
• Erosion
Morphology
Vegetation
• Establishment
• Growth
• Mortality
Photo: S. Dzimballa
Salt Marshes Characteristics

5. 5
Numerical modelling to …
• Further understand complex interactions
• Simulate future salt marsh development
• Support the design of artificial structures to protect salt marshes
• Design nature-based flood protection

6. NBSDynamics
6
NBSDynamics Module
- GitHub
Biota – Models
‘biota specific models’
Coral
Based on Hendrickx et al.
(2021)
Salt Marsh
Vegetation
Based on Bruckner et al. (2019)
Mangroves
Based on Xie et al. (2020)
Hydro- &
Morphodynamics
• Object-oriented python project
• Coupled to Delft3D FM through the BMI

7. NBSDynamics
7
NBSDynamics Module
- GitHub

8. Model Structure
8
Deltares (2021)

9. Vegetation Module
9
Colonization
Development
Mortality
• Random seedling
• Establishment
• Vegetation growth
• Diffusion
• Competition (3 species)
• Bed shear stress
• Inundation

10. Use Cases – Zuidgors Rejuvenation
10
• Vegetation reestablishment after excavation for rejuvenation
Jasper Dijkstra

11. Use Cases – Zuidgors Rejuvenation
11
Jasper Dijkstra
• Test different scenarios for higher biodiversity in the excavated area
→ Excavation design has an impact on species establishment and species diversity

12. 12
“Understand salt marsh and mudflat dynamics in natural
systems, under future pressures, and how they can be
influenced by human interventions.”
0 50 yrs. 0 50 yrs.
Pim Willemsen
Vasileios Kitsikoudis
Bas Borsje
Denie Augustijn
Use Cases - Ongoing Research

13. Use Cases - Ongoing Research
13
Pim Willemsen
Vasileios Kitsikoudis
Bas Borsje
Denie Augustijn
Photo: S. Dzimballa
Photo: S. Dzimballa
Photo: S. Dzimballa

14. Use Cases - Ongoing Research
14
Pim Willemsen
Vasileios Kitsikoudis
Bas Borsje
Denie Augustijn
Photo: S. Dzimballa
Photo: S. Dzimballa
Photo: S. Dzimballa
• - 2 m at sea boundary
• 1 m at landward
boundary
• Linearly increasing bed
level
• Grid cells 5x5 m
• Cohesive sediment
• Flow domain: 2.5 x 1
km

15. Use Cases - Ongoing Research
15
→ Effect of shorter-term dynamics (e.g. seasonal) on long-term salt marsh development
Cliff erosion due to wave power
Non-uniform critical bed shear stress
for erosion and plant mortality
Additional species and interspecies
interactions
Seasonal vegetation dynamics
Pim Willemsen
Vasileios Kitsikoudis
Bas Borsje
Denie Augustijn
Photo: S. Dzimballa
Photo: S. Dzimballa
Photo: S. Dzimballa
Photo: S. Dzimballa

16. Future Improvements
16
• More parameters for exchange through BMI (e.g. wave power, vegetation drag
coefficient)
• More cumulative parameters for exchange (e.g. min values)

17. Thank you!
NBSDynamics Module
- GitHub
Connect on Linkedin
Acknowledgments:
Gijs Hendrix (TUDelft), Peter Herman (Deltares,TUDelft), Jasper Dijkstra (Deltares), Débora deToledo
Alves (Utrecht University), Maarten Kleinhans (Utrecht University), Carles Soriano Pérez (Deltares), Pim
Willemsen (Deltares), Bob Smits (Deltares), and more…

18. References
18
Brückner, M. Z. M., Schwarz, C., van Dijk, W. M., van Oorschot, M., Douma, H., & Kleinhans, M. G. (2019). Salt Marsh Establishment
and Eco-Engineering Effects in Dynamic Estuaries Determined by Species Growth and Mortality. Journal of Geophysical Research:
Earth Surface, 124(12), 2962–2986. https://doi.org/10.1029/2019JF005092
Deltares. (2021). NBSDynamics. GitHub. https://github.com/Deltares/NBSDynamics
Hendrickx, G. G., Herman, P. M. J., Dijkstra, J.T., Storlazzi, C. D., &Toth, L.T. (2021). Online-coupling of widely-ranged timescales to
model coral reef development. Environmental Modelling and Software, 143. https://doi.org/10.1016/j.envsoft.2021.105103
Xie, D., Schwarz, C., Brückner, M. Z. M., Kleinhans, M. G., Urrego, D. H., Zhou, Z., & van Maanen, B. (2020). Mangrove diversity loss
under sea-level rise triggered by bio-morphodynamic feedbacks and anthropogenic pressures. Environmental Research Letters,
15(11). https://doi.org/10.1088/1748-9326/abc122