The document discusses 3D water quality modeling using Delft3D FM Suite. It provides the following key points: 1. Delft3D FM allows for flexible mesh grids that can increase resolution in areas of interest while modeling large domains with reduced computation times. It integrates waves, water quality, and other modules. 2. The North Sea is intensely used with increasing pressures on space and ecology from energy transition, sustainable food, and nature conservation. Integrated modeling tools are needed to assess combined effects of large-scale changes. 3. The 3D DCSM-FM model is used to study effects of offshore wind farms and seaweed cultivation on hydrodynamics, nutrients, primary production and higher

1. Lauriane Vilmin, Firmijn Zijl, Anouk Blauw, Luca van Duren, Jos van Gils, Arjen Markus
and colleagues
Delft Software Days – 9 December 2021, 16-17h CET
3D water quality modelling
using Delft3D FM Suite
Examples of energy, food
and nature transition studies
in the North Sea

2. D-Flow Flexible Mesh (D-Flow FM) module
▪ Computation of water levels and currents using a
finite volume solver on unstructured grid
▪ Smart grid resolution:
− increase resolution towards coast
− “zoom in” areas of interest
− model large domains without dramatically increasing
computation times
▪ σ or Z-layer approaches, combination of the two in
the research phase
▪ Fully integrated waves (D-Waves) and water quality
(D-Water Quality) modules
▪ Parallelization
2
Delft
Software
Days
–
3D
water
quality
modelling
using
Delft3D
FM
Suite
 3D DCSM-FM model grid

3. The North Sea ecosystem:
future opportunities and challenges
One of the most intensively used seas in the world
Pressure on space and ecology will continue to
increase in the future
▪ Energy transition
− development of offshore wind
− floating solar panels
▪ Sustainable food supply
− increased regulations for fisheries
− development of (lower trophic) aquaculture
▪ Resilient ecosystems
− pollution mitigation
− nature conservation & restoration
Delft
Software
Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
3
Area division Dutch Continental Shelf, 2016/2017
Source: PBL Netherlands Environmental Agency, 2018. The future of
the North Sea. The North Sea in 2030 and 2050: a scenario study ▼

4. One of the most intensively used seas in the world
Pressure on space and ecology will continue to
increase in the future
▪ Energy transition
▪ Sustainable food supply
▪ Resilient ecosystems
Delft
Software
Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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Global temperature change and uncertainty
Source: Knutti and Sedláček, 2013. Nature Climate Change ▼
The North Sea ecosystem:
future opportunities and challenges

5. The North Sea ecosystem:
future opportunities and challenges
One of the most intensively used seas in the world
Pressure on space and ecology will continue to
increase in the future
Need for integrated tools to predict combined
effects of large-scale changes at the
ecosystem scale
Delft
Software
Days
–
3D
water
quality
modelling
using
Delft3D
FM
Suite
5
Area division Dutch Continental Shelf, 2016/2017
Source: The future of the North Sea. The North Sea in 2030 and 2050:
a scenario study. PBL Netherlands Environmental Agency ▼

6. The 3D Dutch Continental Shelf Model – Flexible Mesh
(3D DCSM-FM)
▪ Model domain
− North Western European Shelf
− 3D unstructured grid, refined towards
the coasts
− Latest version: 50 vertical layers
(z-σ combination)
▪ Forcings
− Atmospheric fields
− Offshore boundaries
− River inputs
Delft
Software
Days
–
3D
water
quality
modelling
using
Delft3D
FM
Suite
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3D DCSM-FM model domain, bathymetry and grid resolution
1 nautical mile = 1.852 km
Yellow: 1/10° x 1/15° ~ 4 nm x 4 nm
Green: 1/20° x 1/30° ~ 2 nm x 2 nm
Blue: 1/40° x 1/60° ~ 1 nm x 1 nm
Red: 0.75’ x 0.5’ ~ 0.5 nm x 0.5 nm
→ 800 m isobath
→ 50 m isobath
→ 200 m isobath

7. North Sea water quality and ecosystem modelling
using the D-Water Quality process library
▪ Inorganic nutrients, organic
matter, dissolved oxygen
▪ Phytoplankton dynamics
(BLOOM module)
− 4 groups: diatoms,
flagellates, dinoflagellates,
Phaeocystis
− 3 ecotypes adapted to
different light and nutrient
limitation conditions
▪ Grazers (Dynamic Energy
Budget module)
Mussels and Ensis on seafloor
Delft
Software
Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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Scheme of D-Water Quality variables and processes
included in the 3D DCSM-FM ecological model 

8. Model results: temperature and salinity
Delft
Software
Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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 Surface salinity and temperature calculated by 3D DCSM-FM

9. Model results: temperature stratification
Delft
Software
Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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Example of model performance for
temperature and temperature
strtatification 

10. Model results: nutrients
Delft
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Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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Winter mean Dissolved Inorganic Nitrogen
(DIN) surface concentrations 2009-2012 ▼
Winter mean Dissolved Inorganic Phosphorus
(DIP) surface concentrations 2009-2012 ▼
Growing-season mean Chlorophyll a
surface concentrations 2009-2012 ▼
dots = ICES data

11. Model results: nutrients
Delft
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Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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Winter mean Dissolved Inorganic Nitrogen
(DIN) surface concentrations 2009-2012 ▼
Winter mean Dissolved Inorganic Phosphorus
(DIP) surface concentrations 2009-2012 ▼
Growing-season mean Chlorophyll a
surface concentrations 2009-2012 ▼
dots = ICES data

12. 1- Top-down approach (WMR)
Vulnerability & Methods to quantify effects
Ecological effects of offshore wind upscaling:
WOZEP
▪ Reduce knowledge gaps on environmental effects of offshore wind farms (OWFs)
in the North Sea
▪ First attempt to quantify potential changes in the ecosystem with coupled physical and
ecological models and assess impacts for priority species
Delft
Software
Days
–
3D
water
quality
modelling
using
Delft3D
FM
Suite
12

13. Ecological effects of offshore wind upscaling:
WOZEP
▪ Reduce knowledge gaps on environmental effects of Offshore Wind Farms (OWFs)
in the North Sea
▪ First attempt to quantify potential changes in the ecosystem with coupled physical and
ecological models and assess impacts for priority species
Delft
Software
Days
–
3D
water
quality
modelling
using
Delft3D
FM
Suite
13
2- Bottom-up approach (Deltares)
 wind,  turbulence from piles

changes in stratification
and sediment re-suspension

changes in nutrient gradients and light availability

changes in primary production

higher trophic levels (Top-down approach)

14. Offshore wind upscaling scenarios
Delft
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Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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 Layout of large upscaling scenario
▪ Estimation of differences
between upscaling
scenario and “base case”
(without windfarms)
▪ 2007 conditions

15. Effects of offshore wind
hypothetical “2050” upsaling scenario
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Days
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quality
modelling
using
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FM
Suite
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 Absolute difference in annual
mean temperature stratification
between upscaling and base
scenarios
Absolute difference in annual
mean primary production 
changes in
hydrodynamics

16. Effects of offshore wind
hypothetical “2050” upsaling scenario
Delft
Software
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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 % difference in annual mean
surface suspended inorganic
material between upscaling and
base scenarios
Difference in annual mean
primary production 
changes in
hydrodynamics
and sediments

17. Effects of offshore wind
hypothetical “2050” upsaling scenario
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Software
Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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▼ Surface Chlorophyll-a concentrations
No OWF
With OWF
▪ Changes in primary production
intensity
▪ Shift in timing of spring bloom at some
locations

18. Next developments on ecological effects
of offshore wind upscaling
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quality
modelling
using
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FM
Suite
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▪ Growth of grazers on pillars: shift from pelagic
grazers (zooplankton) to “benthic” grazers
(e.g. mussels)
▪ More restricted fishing areas
▪ Opportunities for a combination with other
uses
Fouling on foundation at Horns Rev 1 Offshore Wind
Farm (Denmark)
Photo: BioConsult a/s; Source: DONG Energy – Renewables,
2006. HORNS REV 2 OFFSHORE WIND FARM
Environmental Impact Assessment

19. ▪ OWFs= opportunities for combination with large-scale seaweed cultivation
▪ Sector that could boost food security and economy (EU Blue Growth strategy)
▪ Need to harvest at lower trophic levels for higher marine food production
van de Meer, 2002. Nature Food
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quality
modelling
using
Delft3D
FM
Suite
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Future Food: ProSeaweed
▪ But, seaweed cultivation upscaling limited by:
- Physical Carrying Capacity
- Production Carrying Capacity
- Ecological Carrying Capacity
Goal: quantify spatially-explicit effects of seaweed cultivation upscaling
on the Dutch continental shelf on phytoplankton primary production (&
nutrients as driver)

20. New seaweed module
integrated into D-Water Quality
Delft
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Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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▼ Scheme of the MALG seaweed module

21. Delft
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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▪ Growth, N and C uptake, based on
literature
Broch and Slagstad, 2012. Journal of Applied Phycology
▪ Buildup of internal N, P and C pools,
growth of structural biomass
▪ N & P buildup parameterized based on
lab experiments on Dutch seaweed
PhD thesis A. Lubsch, 2018
▪ Growth of fronds throughout the water-
column/effects on individual layers
▼ Scheme of the MALG seaweed module
New seaweed module
integrated into D-Water Quality

22. Cultivation scenarios:
▪ Yield of 1 kg of dry
weight per m2
between Sept 2016
and Sept 2017
▪ S1 – 25% of all
designated OWF
areas
= Total ~800 km2
▪ S2 – 25 km2 in each
OWF
= Total ~200 km2
▪ S3 – 25 km2 within
Borssele OWF
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3D
water
quality
modelling
using
Delft3D
FM
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Future Food: ProSeaweed
Borssele
HK-Z
IJmuiden
TNWE

23. Delft
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Days
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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Winter nutrient
concentrations
Maximum upscaling scenario (S1):
▪ Most intense difference within
largest OWF area (Ijmuiden Ver):
~20% reduction in DIN, 15% in
DIP
▪ Decrease >10% of both DIN and
DIP over >1,500 km2
▪ Decrease >1% over >25,000 km2
for DIN and >40,000 km2 for DIP
Winter DIN
Without seaweed
Winter DIP
Without seaweed
Difference in winter DIP
With-Without seaweed
Difference in winter DIN
With-Without seaweed

24. Delft
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3D
water
quality
modelling
using
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FM
Suite
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Effects on phytoplankton
primary production
Maximum upscaling scenario (S1):
▪ Maximum decrease of ~30% in
Ijmuiden Ver
▪ Decrease >10% over >20,000 km2
▪ Decrease >1% over >55,000 km2
Spring phyto. PP
Without seaweed
Difference in spring
phyto. PP
With-Without seaweed

25. Delft
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3D
water
quality
modelling
using
Delft3D
FM
Suite
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Effects on phytoplankton
primary production
Cultivation over 200 km2 evenly
distributed over OWFs (S2):
▪ Drops up to ~10% around the
OWF area Hollandse Kust Noord-
West
→ importance of farm size
▪ Decrease of >1% over an area of
>35,000 km2
Spring phyto. PP
Without seaweed
Difference in spring
phyto. PP
With-Without seaweed

26. Delft
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Days
–
3D
water
quality
modelling
using
Delft3D
FM
Suite
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Effects on phytoplankton
primary production
Cultivation over 25 km2 at
Borssele (S3):
▪ Maximum drop <2%
▪ Decrease >1% over an area of
3,060 km2 (100 times larger than
the cultivation area)
→ importance of farm location
with respect to each other
Spring phyto. PP
Without seaweed
Difference in spring
phyto. PP
With-Without seaweed

27. New developments on effects of seaweed cultivation
▪ Urgent need for seaweed model validation against in-situ data (follow-up projects)
▪ Investigation of production carrying capacity and ecological impact for higher cultivation
yields to ensure economic viability - van den Burg, 2019
▪ Need for cross-boundary agreements on seaweed cultivation locations and intensity to
avoid exacerbated downstream effects - Van Duren et al., 2019
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▪ Assessment of current and future ecological carrying capacity of
the North Sea with respect to seaweed cultivation
- need to understand interactions with other species in the food
web and future human interventions (e.g. physical effects of
offshore wind, IMTA aquaculture, oyster restoration, etc.)
- need setting an ecologically meaningful thresholds for acceptable
effects

28. Future food & Nature restoration:
FutureMARES
▪ Provide socially and economically viable
actions, strategies and Nature Based
Solutions for climate change adaptation and
mitigation
▪ 3D DCSM-FM used to simulate scenarios of:
− Upscaling of seaweed and mussel cultivation
− Restoration of flat oyster beds (combination of
lab experiments on different oyster strains by
WUR to determine sand Dynamic Energy
Budget modelling)
− In the context of global climate and socio-
economic changes (up to 2100)
Delft
Software
Days
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3D
water
quality
modelling
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Delft3D
FM
Suite
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 Photo: Dick van
Oevelen, NIOZ

29. Coherent thresholds: OSPAR
Internationally coherent threshold values for
eutrophication assessments
▪ Threshold values defined as 50% above pre-
eutrophic historic situation
▪ International comparison between different models
for ‘ensemble’ hindcast
 Insight in model dependent uncertainties
 International support of resulting threshold values
Delft
Software
Days
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3D
water
quality
modelling
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Delft3D
FM
Suite
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30. Concluding remarks
Delft3D FM Suite
=
Crucial tool to address future marine water quality challenges at the large scale
▪ Supports cutting-edge research projects, operational uses and policy decisions
▪ Continuous integration of state-of-the-art system knowledge into the 3D DCSM-FM model
within projects
▪ Development in computation capacity and hybrid solutions will enable increasingly
complex scenario studies
Delft
Software
Days
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3D
water
quality
modelling
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30

31. Thank you for your
attention!
Q&A time
Delft Software Days – 9 December 2021, 16-17h CET