2D and 3D Modeling of heavy metal distribution in wetland groundwater: The
case of Rietvlei Wetland, Cape Town, South Africa.
By
Qhama Kalimashe (219325731)
A treatise submitted in partial fulfillment of the requirements for the degree;
Bachelor of Science Honours (Geology)
in the
Faculty of Science
Nelson Mandela University
Supervisor: Dr Gaathier Mahed
Co-supervisor: Mr B Takashe
November 2023
1
Table of Contents
1
2
CHAPTER 1: INTRODUCTION ........................................................................................ 3
1.1
Preamble ......................................................................................................................... 3
1.2
Problem statement.......................................................................................................... 4
1.3
Aims ................................................................................................................................. 4
1.4
Specific Objectives.......................................................................................................... 4
1.5
Research Questions ........................................................................................................ 5
1.6
Significance of the study ............................................................................................... 5
CHAPTER 2: Literature Review ......................................................................................... 6
2.1
Defining Wetlands .......................................................................................................... 6
2.1
Functions and importance of wetlands ....................................................................... 6
2.2
Properties of Heavy Metals ........................................................................................... 7
2.3
Heavy metals in the environment ................................................................................ 8
2.3.1
2.4
3
Modelling techniques ..................................................................................................... 8
Study Area .............................................................................................................................. 9
3.1
Locality ............................................................................................................................ 9
3.1.1
3.2
3.3
Diep Estuary ............................................................................................................ 9
Geology .......................................................................................................................... 10
3.2.1
4
Sources of heavy metals ............................................................................................ 8
Geohydrology ....................................................................................................... 11
Land cover and Land use ............................................................................................ 12
Reference .............................................................................................................................. 16
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1 CHAPTER 1: INTRODUCTION
1.1 Preamble
A wetland is a low-lying area of land that is either covered with water or saturated, permanently
or seasonally. Wetlands are important ecosystems that offer a wide variety of physical and
economic benefits to the environment and human population. These benefits include, but not
limited to, (i) improving water quality by filtering out toxins, (ii) controlling floods and mitigating
draught by storing excess water during periods of heavy rainfall and releasing the water during dry
periods, (ii) providing opportunities for reactional activities and (iv) fishing. However, despite
their significance wetlands are endangered and undervalued. Wetlands cover approximately 5- 6%
of the earth’s land surface.
The Rietvlei wetland is located within a catchment in the Western Cape province, in South Africa.
The country is facing a persistent water crisis, and it has been reported that it is moving towards
being a “water stressed” country. Western Cape is one of the most affected provinces. Its
population has resorted to excessive groundwater abstraction, and this has resulted in a drop in the
water table and a subsequent drop in water levels in the wetlands. Effective and efficient
management plans require a comprehensive understanding of hydrological and ecological systems
of the wetland. There is a general consensus that the underlying geology of a wetland and its
relationship with the hydrological cycle needs to be understood because if affects the availability,
movement and quality of groundwater.
Generally, wetlands are surrounded by industrial, residential and agricultural areas. These wetlands
face significant challenges due to human activities and land use practices that release toxins, such
as heavy metals, into the environment. The heavy metals tend to end up in the wetlands and they
impede one of the key roles played by wetlands which is to effectively filter water (Adelina et al.,
2010). Increased levels of heavy metals subject a wetland’s vegetation to physiological stress and
stagnant growth, reducing the effective absorbance of metals by these plants (Bullock & Acreman,
2003). Additionally, heavy metals impede the functioning of microbial communities, thus resulting
in microorganisms failing to decompose organic matter and consequently failing to efficiently
filter water (Gariremo et al, 2019). Elevated concentration levels of heavy metals affect
biogeochemical processes in wetland system resulting in an imbalance of carbon, nitrogen, and
phosphorus ratios.
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Despite the above-mentioned
1.2 Problem statement
The Rietvlei is a large freshwater wetland located in the Western Cape Province of South Africa is
surrounded by residential areas, and most importantly, industrial areas which produce toxic heavy
metals such as mercury lead, arsenic, and cadmium into the wetland system (Gariremo et al.,
2019). Earlier studies have found traces of heavy metals in the Rietvlei Wetland’s groundwater
system (Gariremo et al., 2019) (Gariremo, 2022).
Rietvlei is known to be one of South Africa’s biodiversity hotspots, harboring a vast diversity of
bird species (Adelana et al, 2010 as improper waste disposal and, respectivel, re Due to the high
risk of further pollution in the wetland, the ecological functions and the recreational facilities
provided by the wetland are currently endangered by pollution (Adelana et al, 2010). It is very
critical that mitigation measures to protect the wetland’s water quality are urgently considered.
However, to design mitigation measures that suit this wetland system, it is important to identify
and quantify the distribution of heavy metals in the wetland first. Although previous studies have
found traces of heavy metals in Rietvlei, the extent of contamination and the concentration of these
metals within the wetland are not yet fully exploited. Therefore, the current study aims to identify,
quantify, and map the distribution of heavy metals in the Rietvlei wetland groundwater system.
1.3 Aims
This aims of the study are:
1. To identify, quantify, and determine the distribution of heavy metals in the Rietvlei wetland
and groundwater.
2. To determine the possible uses of the water in the Rietvlei wetland and its groundwater as
outlined by the department of water and sanitation.
1.4 Specific Objectives
To achieve the aim(s) of this study three preliminary objectives are set:
1. To model the longitudinal and latitudinal distribution of heavy metals using 2D and 3D
tool such as
2. To assess the toxicity levels of the wetland and groundwater.
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3. To give recommendations on the possible groundwater protection strategies.
1.5 Research Questions
To achieve the objectives of this study the following questions are posed:
1. Which heavy metals are dominant in Rietvlei wetland?
2. What proxies can be used to identify heavy metals in wetlands and groundwater?
3. What are the actual sources of heavy metals in the Rietvlei wetland?
4. What are the toxicity limits of these metals?
5. How can the concentrations of heavy metals in water be quantified and analyzed
effectively?
6. How effective is 2D modelling in representing heavy metal distribution in Rietvlei?
7. How effective is 3d modelling in representing heavy metal distribution in Rietvlei wetland
8. Which mitigation measures can be put in place to prevent further groundwater
contamination?
9. Are these measures adaptable or unique mitigation measures are required for Rietvlei?
10. What are the possible uses of the water as outlined by the department of water and
sanitation?
1.6 Significance of the study
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2 CHAPTER 2: Literature Review
2.1 Defining Wetlands
The Ramsar Convention defines wetlands as “areas of marsh, fen, peatland or water, whether
natural or artificial, permanent or temporary, with water that is static or flowing, fresh, brackish
or salt, including areas of marine water the depth at which at low tides does not exceed six meters”
(Ramsar convention secretariat, 2013). However, despite this inclusive and internationally
applicable definition, several definitions for wetlands have been adopted across regions and
countries due variations in environmental conditions, cultural perspective and legal & policy
frameworks. The South African National Water Act (NWA) defines wetlands as “transitional areas
between aquatic and terrestrial ecosystems, where the water table is usually close to the surface
or occasionally covered by shallow water, enabling the support of vegetation adapted to saturated
soil conditions”. This study will adopt the latter definition.
2.1 Functions and importance of wetlands
Studies have shown that wetlands are often one of the most misunderstood features in the
landscape. They are, sometimes, said to be a waste of land due to various factors such as; lack of
awareness, development pressure from the rapidly growing population and perceived health risks
as standing water is sometimes believed to be a source of diseases such as malaria. While the above
factors hold some truth to them wetlands are, however, one of the most high-functioning
ecosystems, they play a vital role in the environment providing various ecological, economic and
social benefits. These are some of their functions:

Wetlands are famous for their water filtration and purification function, they act as natural
filters, trapping sediments and filtering out pollutants from water. The pollutants include,
but not limited to, heavy metals and pathogens. This crucial function helps in improving
water quality subsequently pushing day zero further and ensuring that the wetland is a
suitable home for some animal and plant species.

Wetlands absorb and store excess water during heavy rain and storms, reducing the risk of
floods and thus regulating water flow and preventing erosion. Also, some are able to absorb
energy from disasters such as hurricanes, reducing their impact on the surrounding
communities.
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
Wetlands are important sites for scientific research and environmental education. They
host a vast array of animal and plant species that can be studied intensively,

Lastly, wetlands are beautiful and can, therefore, provide opportunities for recreational
activities such as birdwatching. Also, they attract tourists thus contributing to the economy.
2.2 Properties of Heavy Metals
Heavy metals, also known as trace elements, are metallic elements with relatively high atomic
weights and densities as suggested by their name. These metals have a lot of physical and chemical
properties that influence their behavior in the environment- specifically wetlands.

Solubility: Heavy metals are soluble in water under certain conditions, their solubility is
dependent on factors such as ph, redox potential, the presence of ligands and specific metal
ions involved. When the heavy metals have dissolved in water, they become highly mobile
and are easily absorbed by wetlands (Dube et al., 2014)

Oxidation States: Heavy metals can exist in various oxidation states allowing them to form
a wide range of chemical compounds with different toxicities and environmental behaviors
(Dube et al., 2019).

Ionic forms: Heavy metals exist in various ionic forms; these forms are said to be readily
absorbed soil making them readily available for wetland absorption (Appenroth., 2010).

Catalytic Activity: Some heavy metals such as mercury can act as catalysts in chemical
reactions (Appenroth., 2010). This is one of the properties that make heavy metals an
essential part of the environment when monitored.

Electronic configuration: The d- orbital of heavy metals is incomplete thus giving them a
unique property such as the ability to form stable compounds and complexes with organic
matter. These complexes increase their solubility and mobility making it difficult for them
to be removed from the environment thus allowing wetlands to absorb them (Dube et al.,
2019).
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2.3 Heavy metals in the environment
Elements are defined as “heavy metals” either due to their high atomic weight or density (Dube et
al., 2017). The term “heavy metals” has a negative connotation to it which often includes toxicity.
However, there is little to no scientific evidence to support this conclusion, therefore, one could
say that the connotation is based on feelings.
The importance and environmental risk of heavy metals may be described with the phrase “doubleedged sword” because these metals are essential for biological, chemical, and geological processes
that support life on earth (Dube et al., 2019). However, when their concentrations exceed the
maximum threshold, then they become fatal to life.
2.3.1 Sources of heavy metals
Heavy metals are introduced into the environment by natural and anthropogenetic activities such
as volcanic eruptions and mining, respectively. The concentration of these metals in soil and water
sources have emerged primarily due common anthropogenic activities such as mining, smelting,
leaching of metals from landfills, livestock manure, automobiles, roadworks, and the use of
pesticides, insecticides and fertilizers.
2.4 Modelling techniques
Metal distribution in groundwater and soil varies drastically such that it is always best to represent
these distributions using both 2D and 3D modelling techniques for a better analysis. The tools that
can be used include, but not limited to, surfer, voxler and python.
Surfer is a useful tool for creating contour maps, surface plots, and 2D visualizations. In this study,
this tool will primarily be used for 2D visualizations. Voxler, developed by Golden Software, is a
3D visualization and analysis software. It is designed to visualize complex datasets, from various
sources including environmental and spatial datasets, and understanding spatial relationships in
three dimensions. In this paper, it will be used to visualize trace elements in groundwater.
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3 Study Area
3.1 Locality
The Rietvlei wetland is located within the large Diep Estuary north of Cape Town, in the Western
Cape, South Africa. The wetland lies on the floodplain of the Diep River before it drains into
Milnerton Lagoon and subsequently, Table View (Figure 1). Previous studies have reported
Rietvlei as the largest temporary vlei in south – western cape covering 561 hectors of wetland
between the Otto du Plessis Drive and Blaauwberg Road bridge.
Figure 1: The Diep estuary comprising of the Rietvlei wetland and Milnerton Lagoon (Google Earth Pro,
10 October 2023).
3.1.1 Diep Estuary
The Diep estuary is defined as the area from the mouth of the estuary to the Blaauwberg Bridge,
which covers an approximate area of 900 hectares (Figure 1). The upper estuary, generally called
the Rietvlei wetland, is flat with a maximum elevation of 2m above average sea level with the
exception of the Flamingo vlei which is said to be 9m deep. The lower estuary, Milnerton Lagoon,
is relatively flat as well and it follows a narrow winding channel from the Southern tip of Rietvlei
to the river mouth.
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3.2 Geology
The predominant geological formations underlying the Diep River catchment belong to the
Malmesbury group (Tygerberg, Moorreesburg, and Porseleinberg). This is interspersed with the
Klipheuwel and Cape granite groups (Figure 2). There are quaternary deposits, such as alluvium,
calcrete and sand on the coastal plane. These deposits overly the bedrock of the Malmesbury group.
The Malmesbury rocks were deposited 560 million years ago on an ancient continental slope by
submarine slumping and turbidity currents. The lithology of this group is characterized by
alternating layers of dark grey fine-grained greywacke sandstone and purple(ish) shale (which
have been intensely folded and deformed) and Bloubergstrand shoreline. Other sediments include
quartzite, chert, basic lava and tuff. Studies show that magma intruded into the Malmesbury group,
about 560 million years ago, in a north – northwest orientation and it is now exposed as the light
grey porphyritic Cape granites. The Klipheuwel group lies along a narrow belt which crosses the
area from Klipheuwel railway station to Klapmuts Hill. The formation is approximately 2,5km
thick and 2km wide. The main sediments of this formation are sandstone and grit with occasional
layers of conglomerate (which are composed of quartzite, greywacke, indurated shale and grit
matrix) and shale.
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Figure 2: Geology of the selected study area (Source: Water Resource Management Plan in the Diep
River Catchment: A Situation Assessment, pg: 11)
3.2.1
Geohydrology
Based on the geology of the catchment, and other important factors, studies show that there are
two distinct aquifers that describe the geohydrology of the area. These are the (i) confined upper
primary aquifer and an (ii) unconfined secondary aquifers. Despite their differences, as mentioned
below, it is worth noting that both aquifers have a potential yield of 0.5 – 2.0 L/s (Figure 3).

Primary Aquifer: This is an unconfined and intragranular aquifer. It is situated within a 2 –
3 m thick surficial scree and alluvial gravel deposits along the coastal plain. The sediments
are subangular – angular and they are well sorted. Campbell et al., (2017) reported that the
primary aquifer is connected to the river and vlei system. It was also noted that the rest
water level (rwl) is shallow thus making it easy for the surrounding communities to drill
boreholes for their personal uses.

Secondary Aquifer: This is a fractured and weathered aquifer; it is located in the underlying
Cape granite and Malmesbury Group rocks. The shale from the Malmesbury group is
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mineralized
and
it,
therefore,
interferes
with
the
aquifers
potential
yield.
Figure 3: Two distinct aquifer systems present at the Diep River catchment (Source: Moocroft, 2019).
3.3 Land cover and Land use
The Diep River estuary is covered with grasslands and water
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Figure 4:
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Methodology
This study used secondary data and this data was analyzed as follows:
The primary data was collected by Gariremo (et al.,2019), several wells were installed randomly
around the wetland. Sediment profiles were logged at each level and sediments of groundwater
were collected using manual boilers. Field water chemistry was taken in-situ and the collected
water was analyzed.
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Metals in the Environment: Analysis by Biodiversity - M.N.V. Prasad - Google Books
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4 Reference
1. Adelana, S., Xu, Y., Vibka, P. (2010). A conceptual model for the development and
management of the Cape Flats aquifer South Africa. Water SA, 36., 1 – 10.
2. Appenroth, KJ. (2010). What are “heavy metals” in Plant Sciences? Acta Physiol
Plant 32, 615–619. https://doi.org/10.1007/s11738-009-0455-4
3. Bullock,A., and Acreman, M.C. (2003). The role of wetlands in the hydrological
cycle. Hydrology & Earth System Sciences, 7 (3), 75 – 88.
4. Dube, A., Zbytniewski, R., Kowalkowski, T., Cukroska, E., and B, buszweski.
Adsorption and Migration of Heavy Metals in Soil. Journal of Environmental
Science. 10 (1), 1-10.
5. Fetter, C. W. (2001). Applied Hydrogeology. (4th ed), New Jersey: Prentice Hall.
6. Gariremo, N. R. (2022). Geohydrological modelling of Rietvlei wetland, Cape
Town: Site characterizations and numerical modeling for water budget
quantification. Master’s thesis. Nelson Mandela University.
7. Gariremo, N.R., Gaathier, M., Lehlohonolo, S., Campbell, R. And Swaartbooi, E.
(2019). Characterisation of the Rietvlei wetland: Implications for Spatial
distributions
of
groundwater
recharge.
Available
at:
https://www.researchgate.net/profile/GaathierMahed/publication/339827432_Characterisation_of_the_Rietvlei_wetland_Implic
ations_for_spatial_distribution_of_groundwater_recharge/links/5e67a726299bf17
44f70ca44/Characterisation-of-the-Rietvlei-wetland-Implications-for-spatialdistribution-of-groundwater-recharge.pdf?origin=publication_detail
(Assessed: 08 June 2023).
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