Swartkops Estuary Ecosystem Assessment

Swartkops Estuary
Port Elizabeth, South Africa
22 April 2017
by
Gary D. Moore
1
Image Source: lighttackle.ca.za

Outline
1. Introduction
2. Physical Setting
a. Watershed, Airshed, Ocean Boundary
b. Estuary
c. Freshwater Inputs
3. Chemical Setting
b. Estuary
4. Biological Setting
b. Estuary
5. Anthropogenic Stresses (such as nutrient, contaminant, habitat
modification, harvesting of fish and shell fish, and corresponding
health of the estuary)
6. Economic Valuation of Ecosystem Services – Swartkops Estuary
7. Resource Governance – National Legal Framework
8. Sustainable Management Plan Outline
a. Programmatic Work Plan (Three Phases)
I. Phase I – Baseline Understanding
II. Phase II – Protective Regulatory Framework
III. Phase III – Monitoring, Reporting, and Monthly Estuary
Review
2

INTRODUCTION
• No comprehensive and integrated information exists about the Swartkops Estuary, located on the
Indian Ocean along the East Cape coast of South Africa, in the City of Port Elizabeth (300,000
population urban; 1.1 million metropolitan area) (Figures 1-3, next two slides).
• Scientific studies completed to date are heavily weighted toward local ecological assessments;
only portions of ecosystem’s flora (Hilmer, T., Talbot, M. and Bate, G.C., 1988) and fauna (Beckley,
L.E., 1983; Beckley, L.E., 1985; Ellender, B.R., Weyl, O.L. and Swartz, E.R., 2011; Marais, D.,
1980; limited trophic relationships (Baird, D. and Ulauowicz, R.E., 1993), broad and general
information (Baird, D., Marais, J. and Martin, A.P., 1988) concerning the physical setting of the
estuary and its relation to the Indian Ocean.
• Regarding anthropogenic impacts, there is recent work on the bioaccumulation of contamination in
fish (Nel, L., Strydom, N.A. and Bouwman, H., 2015).
• No information on the extent and potential importance of the airshed to estuary nutrient and other
pollution types is available, however, regarding the airshed, relevant but fragmented information
was discovered and is presented in this report. Anthropogenic impacts to the ecosystem appear to
be many (based on published literature, news reports, personal communications); important are
concerns of human health risks (including cancer and increased mortalities) from suspected
contamination exposures, e.g., recreational use, fish consumption, and so on) originating from
industrial and/or improper waste management activities in the watershed.
3

4
INTRODUCTION - CONTINUED
Swartkops
Estuary
Source: Google Maps Scale (Approx) 1” = 200 miles
Figure 1
Source: Google Maps Scale (Approx) 1” = 4 miles
Swartkops Estuary
Figure 2

5
INTRODUCTION - CONTINUED
Source: Google Maps Scale (Approx) 1” = 4000 feet
Swartkops Estuary
Figure 3

PHYSICAL SETTING - WATERSHED, AIRSHED, OCEAN BOUNDARY, ESTUARY,
FRESHWATER INPUTS
6
Watershed
• A watershed for the Swartkops Estuary has not yet been defined, i.e., no published
information is available from universities, the Republic of South Africa, or in specialist
scientific literature.
• Lord, D.A. and Thompson, G.A., (1988) describe the Groot Winterhoek Mountains to the west
as the primary watershed (1,342 km^2, approximately) of the Swartkops River.
• Further, these researchers state, “…the Swartkops and Eland Rivers are the prime
contributors of freshwater to the head of the estuary, with a smaller contribution coming from
the Chatty River, directly into the lower reaches of the estuary” ( Figure 4, next slide) (Lord,
D.A. and Thompson, G.A., (1988)). The Groendal Dam is operated on the upper Swartkops
River but its effect on water and sediment discharge to the estuary is unknown.

7
FRESHWATER INPUTS
Figure 4
NOT TO SCALE

8
FRESHWATER INPUTSAirshed
• An airshed of the Swartkops Estuary system has not yet been defined, i.e., no published information
either from universities or the Republic of South Africa, on the potential of commercial / industrial,
residential, automobile exhaust, and other air emission sources and effects on water quality of the
estuary.
• Available information that may influence an airshed to the estuary system (e.g., climate, local and
regional meteorology, regional geomorphology, local and regional land use) is fragmented, some of
which is presented below. An airshed determination is appropriate for the Swartkops Estuary; such a
determination will be influenced by the regional geomorphology, i.e., Central Plateau, Great Escarpment,
proximity to the Atlantic, Southern, and Indian Oceans, and industrial and other air emissions in the
region. The airshed would cross international boarders and, as such, would need to be an international
transboundary airshed since industrial emission sources exist, for example, from the Zambian Copper
Belt (ZCB) located north of the estuary in Zambia (Department of Environmental Affairs, 2012) (Figure 5,
next slide). The ZCB is estimated to discharge 2.2-millon tons of sulphur dioxide annually. Information
on the full and complete emission profile needs to be investigated to understand the risks to the estuary.
• The Republic of South Africa maintains one or more air quality monitoring stations in Port Elizabeth.

9
FRESHWATER INPUTS
The complex airshed influencing
the estuary system is
transboundary, incorporating
emissions from neighboring
countries to the north.
Swartkops Estuary

10
FRESHWATER INPUTS
Ocean Boundary
The Swartkops Estuary discharges to the Indian Ocean through a constricted inlet (Baird, D. and Ulauowicz,
R.E., 1993). Tidal influence is a maximum of 1.6 meters (m) (5.25 feet (ft)), tidal prism is approximately 2.88 x
10^6 m^3, and flushing time is approximately 22 hours in Spring (Baird, D. and Ulauowicz, R.E., 1993).

11
Estuary
The following is a summary of descriptive information derived from Lord, D.A. and Thompson, G.A., 1988;
Reddering, J., and Esterhuysen, K., 1988):
• The Estuary is located in a metropolitan center of the City of Port Elizabeth (300,000 population, urban;
1.1 million population metropolitan), with industrial and residential properties location on both the north
and south banks of the estuary and Swartkops River.
• The Estuary is predominately sandy, with wide intertidal and supratidal flats near the confluence with the
Indian Ocean, but becomes muddier with steep banks landward in the upper estuary.
• The tidal length is about 16 kilometers from the mouth (i.e., confluence with the Indian Ocean)
• Average depth is 3 m (9.8 ft)
• Historical reconstruction, based on interpretation of sediment core data, indicates the present-day
estuary is significantly smaller; current day depth at mouth ranges from 3 to 4 m; historically the depth
was closer to 8 m
FRESHWATER INPUTS

12
Freshwater Inputs
The primary sources of freshwater to the estuary are the Swartkops and Elands Rivers, with smaller
contribution from Chatty River (Lord, D.A. and Thompson, G.A., 1988)
FRESHWATER INPUTS

CHEMICAL SETTING - WATERSHED, AIRSHED, OCEAN BOUNDARY, ESTUARY,
FRESHWATER INPUTS
13
Watershed
The information summarized below from Lord, D.A. and Thompson, G.A. (1988) is derived from a paper
documenting the pollution status of the Swartkops Estuary. The chemical setting of the watershed can be
divided by source category: municipal, industrial, and domestic.
• Municipal: sewage discharges (domestic as well as industrial waste water treated)
(RELEASES: bacteria, nutruents)
• Industrial: wool processing plants, tannery, power generation
(RELEASES: thermal, metals (adsorbed to sediments) and aquatic fauna, petroleum
hydrocarbons, chlorinated hydrocarbons)
• Domestic: runoff from laws, effluent from vehicle washing, broken sewer pipes
(RELEASES: fertilizers, lawn treatment chemicals, phosphates, raw sewage)

FRESHWATER INPUTS
14
Airshed
Ambient air may contain a range of pollutants, originating from local, regional, and international
(transboundary) sources, as summarized below (Department of Environmental Affairs, 2012):
• Coal combustion from power generation (RELEASES: particulates, sulphur dioxide, nitrogen oxides, mercury)
• Vehicle emissions from combustion of gasoline and diesel (RELEASES: carbon monoxide, nitrogen oxides
• Industrial emissions from combustion of fossil fuels, especially coal (RELEASES: depends mainly on the combustion of
fossil fuels, especially coal, for electricity generation)
• Domestic fuel combustion (i.e., coal, paraffin, and wood) (RELEASES: sulphur dioxide, carbon monoxide, volatile
organic compounds, particulates)
• Biomass combustion, for example, forest fires for agricultural purposes (RELEASES: carbon dioxide, methane, and
nitrous oxide, carbon monoxide, volitale organic compounds)
• Landfill gas emissions (RELEASES: carbon dioxide, methane, and nitrous oxide, hydrogen sulfide, phenols,
chlorobenzene, carcinogens such as benzene and methylene chloride)
• Tyre burning emissions (RELEASES: a broad range of combustion and incomplete combustion products, particulate
matter)
• Commercial aircraft emissions (RELEASES: carbon dioxide, particulates, nitrogen oxide, carbon monoxide, sulfur
dioxide, and volatile organic compounds)
• Agricultural emissions, e.g., sugar cane industry burns 90% of crop at harvest (RELEASES: carbon monoxide and
particulates)
• Common air pollutants in South Africa are: Sulphur dioxide, nitrogen dioxide, ozone, carbon monoxide, lead, particulate
matter, benzene

FRESHWATER INPUTS
15
Ocean Boundary
Little is known about the chemical quality of the coastal waters of the Indian Ocean at the mouth of the
Swartkops Estuary (locally known as Algoa Bay).

16
Estuary
The information below is summarized from Lord, D.A. and Thompson, G.A. (1988) from their discussion on
pollution occurrence in and near the Swartkops River:
(RELEASES: bacteria, nutrients, toxics)
• Domestic: runoff from laws, effluent from vehicle washing, broken sewer pipes
(RELEASES: fertilizers, lawn treatment chemicals, phosphates, raw sewage)
FRESHWATER INPUTS

17
Freshwater Inputs
The information summarized below from Lord, D.A. and Thompson, G.A. (1988) is derived from a paper
documenting the pollution status of the Swartkops Estuary. Freshwater flows entering the Swartkops Estuary
receive pollution from three primary sources and types: municipal, industrial, and domestic.
(RELEASES: bacteria, nutrients, toxics)
• Domestic: runoff from laws, effluent from vehicle washing
(RELEASES: fertilizers, lawn treatment chemicals, phosphates)
FRESHWATER INPUTS

BIOLOGICAL SETTING – WATERSHED, AIRSHED, OCEAN BOUNDARY, ESTUARY,
FRESHWATER INPUTS
18
Watershed
Because of the estuary’s location (in a developed, urban area) consisting of residential and industrial
properties, much of the biodiversity has been removed. However, the headwater of the Swartkops River is
located in the Groot Winterhoek Mountains, part of the Cape Floristic Region. The CFR is recognized as
one of the most floristically diverse areas on earth (WWF, 2017) containing some 9,000 species. “While
vertebrate diversity may not be particularly distinctive”, the area is home to a variety of insects, many of
which “may be Gondwanaland relicts” (WWF, 2017).

19
Airshed
At least 1,000 bird species inhabit southern Africa
(Maclean, G.L. and Robert, A.,1985).
Source: Penguin Books of South Africa
FRESHWATER INPUTS

20
Ocean Boundary
Algoa Bay’s biodiversity attracts both sightseers and researchers. Below is a summary of marine species
and birds to be found in the Bay (Raggy Charters, 2013; Marine Reserves Coalition, ND):
Summary of Biodiversity of Algoa Bay, South
Africa
Southern right whale (Eubalaena austrailis)
Humpback whales (Megaptera novaeanglia)
Bryde’s whales (Balaenoptera edeni)
Bottlenose dolphin (Tursiops aduncus)
Common dolphin (Delphinus capensis)
African penguins (Spheniscus demersus)(endangered)
Cape gannets (Morus capensis)
Cape cormorant (Phalacrocorax capensis)
White-breasted cormorant (Phalacrocorax lucidus)
Africa black oystercatcher (Haematopus moquini)
Southern elephant seal (Mirounga leonine)
Great white shark (Sphyrna zygaena)
Spotted ragged-tooth shark (Carcharius Taurus)
Common thresher shark (Alopias vulpinus)
Smooth hammerhead shark (Sphyrna zygaena)
quini)
Kelp gull (Larus dominicanus)
Sub-antarctic skua (Stercorarius antarcticus)
Swift tern (Thalasseus bergii)
Common tern (Sterna hirundo)
Roseate tern (Sterna dougallii)
Sandwich tern (Thalasseus sandvicensis)
Artic tern (Sterna paradisaea)
Indian yellow-nosed albatross (Thalassarche carteri)
Shy albatross (Thalassarche cauta)
White-chinned petrel (Procellaria aequinoctialis)
Northern giant petrel (Macronectes halli)
Wilson’s storm petrel (Oceanites oceanicus)
Cory’s shearwater (Calonectris borealis)
Sooty shearwater (Ardenna griseus)
Cape fur seal (Arctocephalus pusillus)
Sub-antarctic fur seal (Arctocephalus tropicalis)
FRESHWATER INPUTS

21
Estuary
The Swartkops Estuary is habitat for flora and fauna existing in the unique conditions of variable salinity, daily
currents and flow exchanges with Algoa Bay. A summary of the organisms that comprise the ecosystem is
presented below, based on Gilchrist, J., 1918; Marais, D. and Baird, D, 1980; Baird, D.,1988; Beckley, L.E.,
1985; Baird, D. and Ulauowicz, R.E., 1993; Ellender, B.R., Weyl, O.L. and Swartz, E.R., 2011; Hilmer, T., et
al.,1988; Pierce, S.M., 1983. This information is best summarized in a table organized generally by type and/or
habitat (see Table 1, below).
FRESHWATER INPUTS

22
Planktonic Ichthyo Plants
Microplankton (68-77%,
dominant) (circa 1984-1987)
Nano and Pico plankton
Bacteria
Microflagellates
microzooplankton
Spotted grunter (Pomadasys commersonni)
Lithognathus lithognathus
Argyrosomus holoepidotus
Lichia amia
Pomatomus saltatrix
Family Gobiidae
Round herring (Gilchristella aestuarius)
Sea catfish (Tachysurus feliceps)
Family Mugilidea
Elops machnata
Bartail flathead (Platycephalus indicus)
Eel grass (Zostera
capensis)(extirpated circa
1983?)
Rice grass (Spartina
maritima) (Dominant on
saltmarsh)
Spartina trichochia
Other
Nematodes
Macrobenthos
Mud prawns (Upogebia Africana)
Sand prawn (Callianassa kraussi)
Saltmarsh Fauna
Crab (Sesarma catenata)
Crab (Cleistostoma
edwardsii)
Mollusc (Assiminea
bifasciata)
Zooplankton
Copepods
Mysids
Avian (35 species) (top four energy requirements
are listed
Kelp gull (Larus dominicanus)
Grey plover (Pluvialis squatarola)
Whimbrel (Numerius phaeopus)
Common tern (Sterna hirondo)
Estuary
Species summary Table 1.
FRESHWATER INPUTS

23
Freshwater Inputs
Little information is available about the ecosystem of the Swartkops River, a primary source of freshwater
to the estuary. However, what is know is that the Swartkops receives urban drainage and effluent
discharges from a variety of industrial and waste water sources along the river. In addition, flow in the
Swartkops is regulated by the Groendal Dam, built circa 1934. The impounded water continues to be the
primary source of drinking water to the City of Port Elizabeth. The other main freshwater source – the
Elands River, has a confluence with the Swartkops just prior to entering the estuary. Similarly, little is known
about the ecology of the Elands River other than the tourist information readily available that describes the
headwater area of the river as pristine outdoor/wilderness area with plenty of choice for lodging and
recreation activities.
FRESHWATER INPUTS

ANTHROPOGENIC STRESSES
24
Anthropogenic Stresses
Not surprisingly contamination of the estuary has received much of the research attention. There is
information available in the literature describing myriad anthropogenic stresses on the estuary (Strydom,
Nadine, 2014; Emmerson, W.D., 1985; Lord, D.A. and Thompson, G.A.,1988; Nel, L., Strydom, N.A. and
Bouwman, H., 2015 – from nutrient pollution to contamination of sediments and fish with metals and other
industrial chemicals. This information is best presented in table form (Table 2, see next two slides).Table 2
includes a column of the possible corresponding health impacts for each contaminant type.

ANTHROPOGENIC STRESSES (CONTINUED)
25
Contamination Type
Nutrient Organic, Inorganic,
Physio-chemical
Effects on Health of Estuary
Thermal plume (cause: power
plant effluent)
Habitat destruction, species extirpation,
increased species mortality, species
isolation, tropic structure disruption
Lower pH; cause: anti-fouling
chemicals discharged with
power plant effluent
O2 (dissolved); severe
depletion; cause: discharge
of anti-fouling chemicals from
power plant
Phosphate (Aug,
Nov, Oct) cause:
urban runoff, sewer
overflow
Severe dissolved oxygen depletion in the
head waters; Potential for algal growth
cycle creating depleted dissolved oxygen
conditions; Habitat destruction, species
extirpation, increased species mortality,
species isolation, tropic structure
disruption
Ammonia, nitrate,
nitrite (from
suspected overflow
at Uitenhage sewage
treatment plant);
cause: runoff, sewer
overflows
Potential for algal growth cycle creating
depleted dissolved oxygen conditions;
Anthropogenic Stresses
Summary Table 2.

ANTHROPOGENIC STRESSES - CONTINUED
26
Phosphorus
(deep/bottom
water, in Aug and
Oct 1981) (in low
dissolved O2
conditions; cause:
runoff, sewer
overflow
Potential for algal growth, creating
negative feedback loop with
depleted dissolved O2 conditions;
Habitat destruction, species
extirpation, increased species
mortality, species isolation, tropic
structure disruption
Lead, Cadmium, PCBs,
Mercury; causes: industrial
effluent
Present in juvenile fish and bird eggs
(PCBs); increase species morbidity
and mortality, tropic structure
disruption; human exposure risk from
ingestion
Escherichia coli (bacteria);
cause: untreated sewage
runoff
Unknown on estuary; human risk
from ingestion and dermal contact.
t-DDT (in fish); cause:
industrial runoff, effluent
increased species mortality, tropic
structure disruption, eventual species
extirpation; human risk from ingestion
PCBs (in fish); cause:
industrial runoff, effluent
increased species mortality, tropic
structure disruption, eventual species
extirpation; human risk from ingestion
Contamination Type
Nutrient Organic, Inorganic,
Physio-chemical
Effects on Health of Estuary
Anthropogenic Stresses (continued)
Summary Table 2.

ECONOMIC VALUATION OF ECOSYSTEM SERVICES – SWARTKOPS ESTUARY
27
• Historically the Swartkops Estuary has provided valuable natural services to its users and the
surrounding communities.
• In 2007 an attempt to quantify the value of ecosystem services derived from the Swartkops Estuary was
performed by Turpie and Clark (2007).
• Turpie and Clark (2007) estimated the Swartkops Estuary provides total ecosystem services valued up to
RS$ 150 million per year.
• According to the economic analysis by Turpie and Clark (2007), most of the economic value is derived
from ecosystem services to the recreation sector (which, according to the definition ‘recreation’ used in
the study included the economic value of tourism)
• Notably missing from the economic analysis of Turpie and Clark (2007) was added valuation of the
benefits received from the use of the estuary for both municipal and industrial waste water treatment
and disposal (this omission is, perhaps, a stark indicator of the apparent regional indifference and lack
of a complete understanding of estuary function, science, and value).

RESOURCE GOVERNANCE – NATIONAL LEGAL FRAMEWORK
28
• Recent legislation in the Republic of South Africa, i.e., the Integrated Coastal Management Act (ACT 24,
2008) (ICM), has helped to increase awareness of the importance of estuaries
• The ICM required the preparation of estuary management protocols, i.e., an estuary management plan
which recognized both the importance and need to sustain a healthy resource, within four years of ICM
issuance for every estuary in South Africa.
• In spite of this recent advancement, legacy issues of sediment contamination, historical ecosystem
disruption, ongoing inappropriate uses of the resource, e.g., effluent discharges, from ‘business as
usual’ attitude and practice remain (Personal Communications, 2016/17).
• Some analysts point to the extremely complicated multi-tier and vast government bureaucracy
combined with weak institutions (i.e., institutions which rely on the party/person in power to guide
organizational decisions rather than strong autonomous decision making based on established policy
and/procedure, as reasons for the situation.

29
RESOURCE GOVERNANCE – NATIONAL LEGAL FRAMEWORK (continued)
• In addition, there is an absence of legislation, both national and local, to restore estuaries damaged
from historical use. The true reasons for this are not known, however, after extensive review of
published information and personal communications with affected persons, the following can be
noted:
• There is a significant lack of understanding of the fundamental science of estuary systems and
function.
• The convenient legacy practices of using the estuary and freshwater input streams as effluent
treatment and disposal persist.

30
RESOURCE GOVERNANCE – SUSTAINABLE MANAGEMENT PLAN OUTLINE
The following actions are recommended to sustainability manage the Swartkops Estuary:
Programmatic Work Plan (three phases)
(Phase I – Baseline Understanding; Phase II – Protective Regulatory Framework; Phase III – Monitoring, Reporting, and
Monthly Review)
As necessary, a multi-country Swartkops Estuary governing commission shall be formed.
The Programmatic Work Plan shall be immediately funded with local and national taxes on ecosystem services used.
The Programmatic Work Plan will take legal precedence over all existing law.
Phase I – Baseline Understanding
Comprehensive scientific investigation of the estuary
Tasks
-Define history of formation
-Define historical to contemporary morphology, hydrology, physics, and chemistry of the estuary and all
freshwater and salt water inputs (watershed scale)
-including historical and contemporary hydrologic mass balance accounting for all inputs
-Define historical to contemporary study of/accounting of all ecosystems, all species
-Define historical to contemporary ocean interaction
-Define the airshed for the estuary
-Define the seasonality of the airshed
-Account for the chemistry of the airshed
-Account for all anthropogenic impacts to the estuary (comprehensive, at estuary watershed scale)
-Including accounting of all sources and loading quantity and chemicals
-Ecosystem services economic analysis to assess importance to estuary watershed
Based on the results of the Phase I investigation, Phase II will provide estuary-specific, science-based tasks/milestones for
estuary restoration and sustainable management.

31
(continued)
Monthly Estuary Review)
Phase II – Protective Regulatory Framework
(Goals: restoration and protection of the Swartkops Estuary to ensure continued operation for future generations).
Tasks
-Establish optimal estuary conditions through permitting, operational modifications, e.g., dam, WWTPs, and
broad new enforcement actions, ensuring all hydrologic and sediment inputs to the estuary are seasonally
complete and optimal.
-Prepare and implement restoration plans. For all areas identified in Phase I as degraded, restoration shall be
immediately done.
-Establish a comprehensive discharge permit program for all sources of discharge within the estuary’s
watershed; only discharge concentrations up to an allowable, estuary-specific and science-based
concentration shall be allowed.
-Establish a comprehensive air discharge permit program for on all source of air discharge within the estuary’s
airshed that may effect the water quality of the estuary; as necessary, international agreements will be
implemented.
-Public involvement shall be encouraged for all aspects of estuary governance.
-Public, industry, and government education of the importance of the estuary will be extensive.
-Severe economic and criminal penalties will be enacted for violation of any permit terms. Prosecution in the
International Criminal Court will be sought for permit violation outside South Africa.

32
(continued)
Monthly Estuary Review)
Phase III – Monitoring, Reporting, and Monthly Estuary Committee Review
-Prepare Sampling and Analysis Plan (SAP); Data collection quality control plan; Data analysis plan
-Establish permanent monitoring network
-Establish continuous flow gauging stations with telemetry control/reporting, where possible
-Collect, analyze, and report samples; prepare monthly reports
-Indicator samples of ecosystem health and biological/species health
-Water quality, nutrients, salinity (all samples shall be multi-depth, see SAP)
-Samples shall characterize the full (for all seasons)estuary hydrologic system, i.e., freshwater
inputs, estuary flow, saltwater inputs
-Flow within the full estuary hydrologic system (multi-level) shall be monitored (for all seasons)
-Air samples shall characterize the daily variation in air quality within the estuary’s airshed
-All permitted discharges within the estuary’s watershed shall be monitored, and effluent discharge reports
reviewed monthly; percent of actual sites will be audited for compliance monthly.
-On a monthly basis, the Committee will review progress made toward restoration, and will implement
changes to the Programmatic Work Plan as necessary to ensure the optimal and timely achievement of
program goals.

33
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34
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