17 B : Benthic Specification
The CSIEM platform has been designed to accommodate horizontal variation in benthic substrates. This is needed to be able to resolve:
- the effect of bottom roughness on flow dynamics
- the variation of sediment properties, as relevant to sediment transport dynamics
- variability in the dynamics of sediment biogeochemical processes.
- the dynamics of bottom biotic communities, and their associated feedbacks to water column properties
Bottom properties are configured via setting of a) material zones and b) relevant benthic or sediment properties. This is done via loading shape files into a CSIEM simulation, and/or files with cell-specific BGC properties (“benthic_maps”).
17.1 Benthic mapping data sources
The CSIEM benthic substrate (material zone) maps are based on a combination of sediment and biotic data-sets. The two main biotic data-sets are:
- WWMSP Theme 2.1 CSOA data product : recent benthic mapping as reported in Hovey et al. (2024) (Figure 17.1)
- O2M-Westport CSOA EIA data product: an updated benthic map with additional benthic categories to WWMSP 2.1 mapping, including filter feeders and sparse/ephemeral seagrass. The classification of several dominant seagrass communities in this map differs to the WWMSP2.1 mapping (Figure 17.2). This product also includes a separate substrate map (abiotic)(Figure 17.3).
The main sediment/substrate data-set is:
- Skene et al. (2005) : interpolated sediment size data from within CS (Figure 17.4)
Since the available sediment physical and benthic habitat mapping in the above three mapping records is focused around the main Cockburn Sound and Owen Anchorage area, there are areas in the overall CSIEM domain that are do not have known habitat or substrate types. Therefore, additional datasets were considered including:
- WC Bioregion survey : broadscale benthic habitat mapping product (Figure 17.5)
Figure 17.1. WWMSP Theme 2.1 CSOA benthic habitat map.
Figure 17.2. O2M-Westport CSOA EIA benthic habitat map.
Figure 17.3. O2M-Westport CSOA EIA substrate map.
Figure 17.4. Sediment size map within CS.
Figure 17.5. WCB bioregion benthic map.
17.2 Benthic zone definition and layer descriptions
The above raw data-sets require processing and merging before they are suitable for the CSIEM numerical model. Therefore, a synthesised product has been made for each fo the main CSOA benthic maps (Figure 17.6).
The benthic model is able to support layering such that default properties can be specified broadly across the domain, and where more accurate mapping data is available (i.e., within the main Cockburn Sound area) then these layers will supersede the defaults. The layering adopted in this model is shown in Figure 17.7.
Two map versions (WWMSP2 and O2M) are available and can be selected during configuration. Note that the high resolution mapping of benthic habitats from the Hovey et al., 2024 and O2M-Westport data-set is smoothed, to simplify the complexity of the shapefile for alignment with the TUFLOW-FV mesh resolution.
Depending on the mesh adopted, the layer information is translated to cell resolution accordingly, for example, as shown in Figure 17.8 for the three main types.
Each benthic layer/type in the shapefile has a unique ID (material zone ID, Table 17.1) which can be used by TUFLOW-AED for model parameter configurations, or used by matlab scripts for processing (e.g. creating the AED benthic variable parameter csv by assigning parameters to each grid cell based on the zone ID it falls in using assign_mesh_material_zones_allvars.m, Figure 17.6).
Figure 17.6. Workflow illustrating how raw benthic datasets were synthesised and used to parameterise the spatially resolved model.
WWMSP 2.1
Figure 17.7-i. CSIEM model domain and material zone settings based on WWMSP2.1 mapping. Left: whole model domain; Right: zoom-in view of Cockburn Sound.
WWMSP2.1-O2M merged
Figure 17.7-ii. CSIEM model domain and material zone settings based on merged WWMSP2.1-O2M mapping. Left: whole model domain; Right: zoom-in view of Cockburn Sound.
Figure 17.8. Plan-view of CSIEM model benthic material types around the Cockburn Sound region in A (coarse), B (optimized), C (fine) options.
17.3 Zone parameterisation
A summary table of key parameters for each benthic zone is summarised in Table B.1.
| Material zone ID | Name | Note | Sediment Functional Zone (1) | Roughness (m) (2) | Sediment-Water flux (mmol/m2/day) (3) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Oxygen | PO4 | NH4 | NO3 | DOC | DON | DOP | |||||
| 1 | Default model domain background | Not used, just captures any unallocated cells if shapefiles are do not fully overlap | 0.02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| 16 | Swan River | non-vegetated lower Swan estuary sediment | Type 2: deep basin | 0.004 | -40 | 0.08 | 0.4 | 1.3 | -52 | -5.2 | -0.4 |
| 21 | Cockburn (23-31) | sediment grain size (uM), from Skene et al (2005) | Type 2: deep basin | 0.001 | -45 | 0.09 | 0.45 | 1.5 | -60 | -6 | -0.44 |
| 22 | Cockburn (31-63.5) | sediment grain size (uM), from Skene et al (2005) | Type 2: deep basin | 0.002 | -40 | 0.08 | 0.4 | 1.3 | -52 | -5.2 | -0.4 |
| 23 | Cockburn (63.6-125) | sediment grain size (uM), from Skene et al (2005) | Type 2: deep basin | 0.004 | -40 | 0.08 | 0.4 | 1.3 | -52 | -5.2 | -0.4 |
| 24 | Cockburn (125-250) | sediment grain size (uM), from Skene et al (2005) | Type 3: shelf + MPB | 0.008 | -40 | 0.08 | 0.4 | 1.3 | -52 | -5.2 | -0.4 |
| 25 | Cockburn (250-350) | sediment grain size (uM), from Skene et al (2005) | Type 3: shelf + MPB | 0.01 | -35 | 0.07 | 0.35 | 1.12 | -44.8 | -4.48 | -0.36 |
| 26 | Cockburn (350-500) | sediment grain size (uM), from Skene et al (2005) | Type 3: shelf + MPB | 0.015 | -30 | 0.06 | 0.3 | 1 | -40 | -4 | -0.32 |
| 27 | Cockburn (500-1000) | sediment grain size (uM), from Skene et al (2005) | Type 3: shelf + MPB | 0.02 | -25 | 0.05 | 0.25 | 0.8 | -32 | -3.2 | -0.24 |
| 59 | Artificial structure | 0.2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| 60 | Seagrass (Swan River) | Halophila dominant community | Type 4: shelf + seagrass | 0.1 | -5 | -0.012 | -0.06 | -0.18 | 0 | 0 | 0 |
| 61 | Soft substrate (Sand) | Type 1: offshore | 0.008 | -15 | 0.03 | 0.15 | 0.5 | -20 | -2 | -0.16 | |
| 68 | Hard substrate (Reef with macroalgae) | 0.1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| 70 | Mixed substrate | 0.05 | -10 | -0.02 | -0.01 | -0.03 | 0 | 0 | 0 | ||
| 90 | Seagrass (Amphibolis) | Type 4: shelf + seagrass | 0.1 | -5 | -0.012 | -0.06 | -0.18 | 0 | 0 | 0 | |
| 91 | Seagrass (P australis dominant community) | merged from categories "P. australis", "P. australis Amphibolis", "P. australis P. sinuosa", "P. australis P. sinuosa Amphibolis" | Type 4: shelf + seagrass | 0.1 | -5 | -0.012 | -0.06 | -0.18 | 0 | 0 | 0 |
| 92 | Seagrass (P coriacea dominant community) | merged from categories "P. coriacea", "P. coriacea Amphibolis", "P. coriacea Amphibolis with Halophila" | Type 4: shelf + seagrass | 0.1 | -5 | -0.012 | -0.06 | -0.18 | 0 | 0 | 0 |
| 93 | Seagrass (P sinuosa dominant community) | merged from categories "P. sinuosa", "P. sinuosa Amphibolis", "P. sinuosa P. coriacea Amphibolis" | Type 4: shelf + seagrass | 0.1 | -5 | -0.012 | -0.06 | -0.18 | 0 | 0 | 0 |
| 94 | Lyngbya | this may be updated at a later stage by Theme2.1 as it could be interspesed with ephemeral seagrass | Type 4: shelf + seagrass | 0.1 | -5 | -0.012 | -0.06 | -0.18 | 0 | 0 | 0 |
| 95 | Cobble | Type 3: shelf + MPB | 0.1 | -5 | -0.012 | -0.06 | -0.18 | 0 | 0 | 0 | |
\(1\) the sediment functional zone is associated with the types specified in the sediment biogeochemistry model;
\(2\) For roughness, CSIEM used the 'ks' bottom drag model, in which the values are 'equivalent Nikuradse roughness (m)';
\(3\) The Sediment-Water flux settings are assumed maximum fluxes in each zone combining sediment survey data (Eyre et al., 2025) and relevant environmental factors. The final modelled fluxes are also subject to oxygen concentration (redox potential) and temperature within the bottom water.