Presentation by João Pinheiro (University of Aveiro, Portugal), at the Delft3D User Days, during Delft Software Days - Edition 2022. Monday, 14 November 2022.

1. Salt Intrusion Modeling in Aveiro Lagoon under Morphological
and Climatic Changes
João Pinheiro
(joaoppinheiro@ua.pt)
Advisor: Dr. João Miguel Sequeira Silva Dias, NMEC (CESAM), University of Aveiro
Co-Advisor: Dr. Edward Stephen Gross, CWS/UCD, University of California
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2. 1. Overview
2. Ria de Aveiro: basic classifications
3. Aveiro Lagoon 3-D Model set-up
4. Model calibration
5. Ongoing work
6. References
Outline
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3. • It is widely known that both climate change and morphological modifications induced
by direct human actions are currently affecting tidally dominated coastal environments
by changing estuarine circulation patterns and enlarging tidal amplitude and salt
intrusion
• Particularly, saltwater intrusion increase is a critical concern because it may impacts
estuarine ecology, compromising biological populations abundance, composition and
distribution (Spalding et.al., 2007)
• Furthermore, an upstream migration of saline fronts
could also affect the estuary water quality limiting its use
for human purposes, such as agriculture, industry and
human supply (Rice et.al., 2012)
Overview: Worldwide salinity patterns changes
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4. • Aveiro Lagoon has been subject to several studies concerning the impact of climate
change (projected mean sea level rise and river inflow) as well as of local morphologic
modifications (dredging operations) on main physical patterns and dynamics. However,
none of these studies researched the local 3-D salinity structure and concern on how
the salinity distribution patterns:
Overview: Case study (Aveiro Lagoon)
1. depend on the physical processes
2. are being affected by morphological
modifications comparing to climate change
3. will be in future as a result of dredging
operations and climate scenarios
SALINITY
CHANGES
River
Inflows Human
Actions
Mean
Sea
Level
Rise
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5. Overview: Questions
• How are salinity patterns changing?
• Why are they changing?
• How will they change in future?
• How are morphological modifications changing salinity patterns?
• How are salinity patterns expected to adjust in a climate change context?
• Are the saline disturbances induced by morphological modifications significant
comparing with those induced by climate change?
• What are the main physical mechanisms involved in salt transport?
• How are these mechanisms controlling salt intrusion under a climate
change context and human influence?
• Are these mechanisms changing and how they will be in future?
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6. Overview: Methodology
• To answer the questions outlined on the previous slide, a summary of the methodology
used is described bellow:
1. Analyze atmospheric and oceanic data from the 6th Assessment Report of IPCC for
present conditions and for future climate scenarios, assessing changes between future
and present climates
2. Develop and explore empirical models to assess salt intrusion lengths
3. Develop and implement a 3D novel hydrodynamic model for Aveiro Lagoon, based on
a world leading 3D modelling suite (Delft3D)
4. Generate schematic and real numerical bathymetric configurations from bathymetric
and topographic data collected during different surveys
5. Calibrate and validate the 3D hydrodynamic model for tidal
elevations, tidal currents and salinity
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7. 6. Define and simulate a set of scenarios based on: 1) projected mean sea level rise and river
flow discharges in a climate change context; 2) changes in Aveiro Lagoon morphology.
Further, schematic morphological configurations will be also established as a test
sensitivity cases, to assess which dredging operations have higher impact on salinity
patterns changes
7. Characterize the main physical mechanisms involved on salt transport under past, present
and future conditions, evaluating the changes that have occurred and that are likely to
occur
Overview: Methodology
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8. Aveiro Lagoon: basic classifications
▪ Coastal lagoon with a very complex geometry
• It connects with the Atlantic Ocean through a single
fixed inlet
• It is 45 km length and 10 km wide
• Ecological relevant and local socio-economical
important
▪ Shallow lagoon
• Average depth of about 1 m
• Average depth in the inlet channel higher than 20 m
▪ Lagoon hydrodynamic is dominated by tides
• Predominantly semi-diurnal (M2)
• Maximum tidal range at the inlet is 3.2 m (spring
tides) and the minimum is 0.6 m (neap tides)
• Mesotidal lagoon
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9. ▪ Freshwater sources
• The average discharge of the river during a tidal
cycle is 1.8 x 106 m3
➢ 76% Vouga river
➢ 13% Mira river
➢ 6 % Antuã River
➢ 3% Boco River
➢ 2% Cáster river
Aveiro Lagoon: basic classifications
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10. ▪ Salt wedge (more pronounced at Espinheiro channel)
• Vaz et. al (2008) found that during the January and
December survey periods at Espinheiro channel, the
regions revealed salt wedge characteristics, with the
establishment of vertical stratification during the flood
period.
• When the river flow is low – less than 10 m3 s−1, the
water column near to the red star is filled with salt water
incoming from the coastal waters.
• When the river flow is higher than 100m3 s−1 vertical
stratification is established along all the channel. The
incoming freshwater from the river extends its influence,
and near the surface, the water is brackish, close to the
lagoon's mouth, with salinity values of about 20 psu.
Aveiro Lagoon: basic classifications
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11. Outubro de 2019
Model set-up: Unstructured mesh
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12. Outubro de 2019
Model set-up: Bed level
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13. Outubro de 2019
Model set-up: Settings
Parameter Value
Code version 1.6.3.50451 (research programme Deltares)
Time step CFL (1)
Vertical layers 20 equidistant/non-equidistant Z-layers (still in progress)
Manning coefficient Spatial varying roughness (Lopes, 2016)
Uniform hor. eddy viscosity 1 (m2
/s)
Uniform hor. eddy diffusivity 1 (m2
/s)
Conveyance2D -1 (bed level at velocity point is mean value of corners)
Bed level type 3 (at nodes, face levels mean of node values)
Advection scheme for momentum 3 Perot q(uio-u)
Limiter type for momentum 4 (Monotone central)
Solver type 4 (SodekGS-Saadilud) / 7 (Parallel/GS)
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14. Outubro de 2019
Model set-up: Model boundary conditions
• Tidal boundary conditions : TPXO 9.0 Global
Inverse Tide Model (last available tidal solution)
The amplitude and phase of each tidal constituent are
interpolated onto the boundary cells of the model. We
are following a methodology described by Rayson et. al
(2015) to compare observations against model results
• Transport boundary conditions :
IBI_ANALYSISFORECAST_PHY_005_001
(ATLANTIC-IBERIAN BISCAY IRISH-OCEAN
PHYSICS ANALYSIS AND FORECAST)
The salinity and temperature are interpolated onto the
boundary cells of the model, as a time series and at
different layers
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15. Outubro de 2019
• Surface conditions : ERA5
We are using ERA to get cloudiness, evapotranspiration/rainfall, 2m dewpoint temperature, 2m
temperature, 10m u and v component of wind. Those variables from ERA are used to prescribe
evapotranspiration/rainfall, air temperature, relative humidity, cloudiness and wind direction and
magnitude. The computed quantities are prescribed at the open boundary as time series.
Model set-up: Model boundary conditions
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• Freshwater inflow : Watershed model SWIM
Possible source of error. There is no “real” measured
flow or temperature at any station except Vouga
river.

16. Outubro de 2019
Model calibration: Close up at lagoon mouth
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17. Outubro de 2019
Model calibration: Close up at lagoon mouth
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18. Outubro de 2019
Model calibration: Close up at Espinheiro branch
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19. Outubro de 2019
Model calibration: Close up at Espinheiro branch
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20. Outubro de 2019
Model calibration: Close up at São Jacinto branch
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21. Outubro de 2019
Model calibration: Close up at São Jacinto branch
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22. Outubro de 2019
Model calibration: Close up at Ílhavo branch
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23. Outubro de 2019
Model calibration: Close up at Ílhavo branch
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24. Outubro de 2019
Model calibration: Close up at Mira branch
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25. Outubro de 2019
Model calibration: Close up at Mira branch
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26. Outubro de 2019
Model calibration: July 2019
Station 𝑢𝑏𝑅𝑀𝑆𝐸 𝑆𝑘𝑖𝑙𝑙 𝑅2
Barra 0.09 0.9962 0.9875
Vagueira 0.10 0.9936 0.9766
Areão 0.14 0.9750 0.9406
Vista Alegre 0.11 0.9903 0.9721
Cais da Pedra 0.15 0.9772 0.9199
Rio Novo 0.12 0.9934 0.9745
Cais do Bico 0.12 0.9930 0.9750
Torreira 0.06 0.9978 0.9923
Puxadouro 0.17 0.9641 0.8854
Carregal 0.15 0.9860 0.9545
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27. Outubro de 2019
Model calibration: close up at Torreira (T) station
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28. Outubro de 2019
Model calibration: close up at Cais do Bico (CB) station
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29. Outubro de 2019
Model calibration: close up at Vista Alegre (VA) station
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30. Outubro de 2019
Model calibration: Computational performance
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Singularity container
(HPC High Performance Cluster)
20 equidistant Z-layers
ARGUS (some specifications)
• 20 Processing Servers with 2 CPUs of 12
cores @ 2.60GHz, 128 GB RAM and 128 GB
local temporary storage
• low latency network between all servers
• 10 Gbit interconnection to the outside

31. Outubro de 2019
Ongoing work:
• Complete the calibration of the 3-D hydrodynamic model for salinity
• Develop simple models to assess salt intrusion lengths, from historical salinity
data available at NMEC
• Define and simulate scenarios to evaluate the impact of climate change and human
induced modifications on salinity distribution throughout Aveiro Lagoon
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32. Outubro de 2019
References
• Lopes, C. L., 2016. Flood Risk Assessment in Ria de Aveiro Under Present and Future Scenarios.
University of Aveiro
• Rayson, M. D., Gross, E. D., Fringer, O. B., 2015. Modeling the tidal and sub-tidal hydrodynamics in a
shallow, micro-tidal estuary. Ocean Modelling 89, pp. 29-44
http://dx.doi.org/10.1016/j.ocemod.2015.02.002
• Rice, K. C., Hong, B., Shen, J., 2012. “Assessment of salinity intrusio n in the James and Chickahominy
Rivers as a result of simulated sea-level rise in Chesapeake Bay, East Coast, USA,” J. Environ.
Manage., vol. 111, pp. 61–69
• Spalding, E. A., Hester, M. W., 2007. “Interactive effects of hydrology and salinity on oligohaline plant
species productivity: Implications of relative sea-level rise,” Estuaries and Coasts, vol. 30, no. 2, pp.
214–225
• Hong, B., Shen, J., 2012. “Responses of estuarine salinity and transport processes to potential future
sealevel rise in the Chesapeake Bay,” Estuar. Coast. Shelf Sci., vol. 104–105, pp. 33–45
• Vargas, C. I. C., Vaz, N., Dias, J. M., 2017. “An evaluation of climate change effects in estuarine salinity
patterns: Application to Ria de Aveiro shallow water system,” Estuar. Coast. Shelf Sci., vol. 189, pp. 33–
45
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33. Outubro de 2019
• Vaz, N., Dias, J. M., 2008. “Hydrographic characterization of an estuarine tidal channel”, Journal of
Marine Systems, vol. 70, pp. 168–181
References
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