River ecosystems

(Nel, 2011)
NFEPA ([Link]

 National Freshwater Ecosystem Priority Areas (NFEPA) project

o led by CSIR (Council for Scientific and Industrial Research) and SANBI
(South African National Biodiversity Institute)
o aimed to identify a national network of freshwater conservation areas
and to explore institutional mechanisms for their implementation
 1. Identify Freshwater Ecosystem Priority Areas (hereafter
referred to as ‘FEPAs’) to meet national biodiversity goals for
freshwater ecosystems; and
 2. Develop a basis for enabling effective implementation of
measures to protect FEPAs, including free-flowing rivers.

General info freshwater ecosystems

Vulnerability:

 Only 18% of our water supply areas are formally protected

 Freshwater and estuarine ecosystems are highly threatened, respectively,
82% estuarine, 65% wetland and 57% river ecosystem types are threatened
(critically endangered, endangered or vulnerable)

Importance:

 Freshwater ecosystem priority areas are a valuable national asset.

 o = “Managing FEPAs in a good condition is not just about conserving
freshwater plants and animals – it should also be regarded as a
comprehensive approach to sustainable and equitable development of
water resources. Keeping strategically-chosen freshwater ecosystems
in a good condition serves a dual purpose of meeting government
objectives for both sustainable water resource development (National
Water Act) and freshwater biodiversity conservation (National
Environmental Management: Biodiversity Act). The current and
recommended ecological category for all river FEPAs is A or B. Wetland
FEPAs that are currently in a condition lower than A or B should be
rehabilitated to the best attainable ecological condition.”
 Freshwater inputs are critical to estuarine and marine environments.
o = “Fresh water flowing to estuaries and the sea provide important
inputs such as nutrients, sediments and carbon, which in turn maintain
important ecological processes that keep our marine resources healthy.
Healthy marine and coastal ecosystems sustain commercial and
recreational fish stocks, and provide a source of food to poor coastal
communities that depend directly on marine resources for food. A
certain amount of water is also required to scour the mouth of most
estuaries – without this scouring effect, sediments build up at the mouth
and the risk of back-flooding during storms increases. Artificial
breaching of an estuary mouth to minimise this risk is expensive and
damages estuarine ecosystems. This is why water running out to sea
should not be considered wasted.”
 Healthy tributaries and wetlands support the sustainability of hard-working
rivers.
 o = “With effective planning, freshwater ecosystems in a catchment can
be designed to support multiple levels of use, with natural rivers and
wetlands that are minimally-used supporting the sustainability of
heavily-used rivers, wetlands and estuaries that often form the
economic hub of the catchment. Healthy tributaries can improve water
quality by ‘flushing’ pollutants when they join their mainstem rivers, and
they also replenish water supply in the mainstem. Wetlands filter
pollutants and sediments from the surrounding landscape thus
preventing them from entering the river. They also regulate flow of
water from the surrounding landscape which helps to reduce the effects
of flood (by slowing down run-off) and droughts (by reducing
evaporation).”
 Healthy buffers of natural vegetation mitigate the impact of land-based
activities.
o = “Freshwater ecosystems are generally the lowest point in the
landscape, making them the ‘receivers’ of wastes, sediment and
pollutants in runoff. This combined with the strong connectivity of
freshwater ecosystems means that they are highly susceptible to
upstream, downstream and upland impacts. Managing land-based
impacts in the whole catchment is therefore essential. While it is
seldom feasible for entire catchments to be ‘locked away’ from human
use, catchments can be designed to incorporate varying levels of use
and impacts on freshwater ecosystems. Buffers of vegetation
surrounding all freshwater ecosystems, even heavily used ones, go a
long way to reducing the effects of deleterious land-use practices. The
effective width of the management buffer should be determined on a
site-specific basis. The NFEPA implementation manual provides some
recommendations for delineating management buffers”
 Groundwater sustains river flows particularly in dry seasons.
 o = “Groundwater abstracted from river beds, close to streams, and from
shallow alluvial aquifers has a very direct influence on river flow, and
should be not be viewed as an additional water resource. Such
groundwater plays an important role in sustaining wetlands and river
flows (‘base flows’) and supporting refuge pools in the dry season.
Apart from the human benefits of maintaining river flows in the dry
season, refuge pools in seasonal rivers support water-dependent
animals that would otherwise not survive when the rivers dry up.
Healthy riparian areas, which filter pollutants that drain from the land,
are also often maintained by groundwater. It is only when groundwater
has very weak links to surface water (such as in deep, confined
aquifers) that it may be possible to abstract it without significantly
impacting on river flow; however, long-term impacts are not well
understood.”
 Healthy freshwater ecosystems support resilience and adaptation to climate
change.
o = “Healthy natural ecosystems can increase resilience to the impacts of
climate change, by allowing ecosystems and species to adapt as
naturally as possible to the changes and by buffering human
settlements and activities from the impacts of extreme weather events.
Freshwater ecosystems are likely to be particularly hard hit by rising
temperatures and shifting rainfall patterns, and yet healthy, intact
freshwater ecosystems are vital for maintaining resilience to climate
change and mitigating its impact on human well-being. In the western
part of South Africa, which is likely to become dryer, intact rivers and
wetlands will help to maintain a consistent supply of water; in the
eastern part of the country, which is likely to become wetter, intact
rivers and wetlands will be important for reducing flood risk and
mitigating the impact of flash floods.”

Recommendations:
  Employ aquatic ecologists in provinces, Catchment Management Agencies
and local municipalities to promote sustainable water development decisions.
 Use FEPAs in assessing environmental impact assessment applications and
making land-use decisions.
 Use FEPAs in water resource development processes, including water
resource classification, development of catchment management strategies,
water use license applications, resource quality objectives, and ecological
reserve determination.
 Applications for mining and prospecting in FEPAs should be subject to
rigorous environmental and water assessment and authorisation processes,
as mining has a widespread and major negative impact on freshwater
ecosystems.
 Revive the Mountain Catchment Areas Act, which has the potential to play a
much larger role in protecting our water supply areas.
 Strengthen and expand the scope of the River Health Programme to include
wetland and to actively target FEPAs as new monitoring sites.

Area specific recommendations: (Macfarlane, 2014)

Silwerstroom river

REACHCODE: G21A040000
Planning unit identifier (UNIT_ID): 8788
REACHNUM: G108
ORDER_: 1

Mainstem: (0) Tributary that is nested within quaternary

Length: 1149.04 + 1550.50
Name: Silwerstroom
L1-Ecoregion: 24 (South Western Coastal Belt)

 Ecoregion group: Southwestern Coastal Belt & Uplands; Level 1 Ecoregion:

South Western Coastal Belt
  based national Level 1 ecoregions (Kleynhans et al. 2005)
 Ecoregions classify the landscape into 30 categories based on topography,
altitude, slope, rainfall, temperature, geology and potential natural vegetation

L2-Ecoregion: 24_3
Flow variability: P = Permanent or seasonal; here: Perennial/Seasonal

 Permanent seasonal or intermittent rivers only flow during wet periods, drying
up in dry seasons, often fed only by rain or snowmelt
 using flow descriptions in the Department of Water Affairs 1:500 000 rivers and
the 1:50 000 rivers of the Department Land Affairs: Chief Directorate Surveys
and Mapping (2005-2007)

Geomorphic zone: D = Upper foothills

Lumped geomorphic zone: U = Upper foothills, lumping of classes A and B
River type: 24_P_U (L1-Ecoregion_ Flow_ Geomorphic zone)
River condition (by DWA'S PRESENT ECOLOGICAL STATE 1999: C = moderately
modified
River condition (by NFEPA): B = largely natural with few modifications (A or B are
considered intact and able to contribute towards river ecosystem biodiversity targets)

 A small change in natural habitats and biota may have taken place but the
ecosystem functions are essentially unchanged.
 River condition= extent to which the river has been modified by human activity
ranging from natural (A) to critically modified (F)

Free-flowing River ID (FFRID): 0

Lumped ecoregion of free-flowing river: NULL
Flagship free-flowing river: 0
FEPA status (FEPATXT): FEPA = freshwater ecosystem priority area

 indicates that they should remain in a good condition in order to contribute to

national biodiversity goals and support sustainable use of water resources

FEPA status code: 1 = freshwater ecosystem priority area

Water Management Area Silwerstroom:

Silwerstroom:

Slope categories

 ability of river reaches to store or transport sediment, with each zone

representing a different physical template available for the biota
o grouped into four classes for depicting ecological characteristics at a
national level: mountain streams, upper foothills, lower foothills and
lowland rivers
o based on geomorphological zonation work by Rowntree and Wadeson
(1999)

Area general

Density of FEPAs per Water Management Area: 10%

 calculated as % of total area of that Water Management Area that has been
identified as a FEPA or associated sub-quaternary catchment

Density of FEPAs per sub-Water Management Area: ~ 1%

 calculated as % of total area of that sub-Water Management Area that has

been identified as a FEPA or associated sub-quaternary catchment
Free-flowing rivers of South Africa: not Silwerstroom
or rivers without dams that flow undisturbed from their source to the confluence with
a larger river or to the sea

Fish sanctuaries: 0 for Silwerstroom

for threatened and near threatened fish species indigenous to South Africa

High water yield areas: not Silwerstroom (< 100%)

which are sub-quaternary catchments where mean annual runoff is at least three
times more than the average for the related primary catchment

High groundwater recharge areas: not Silwerstroom (100-300%)

which are sub-quaternary catchments where groundwater recharge is at least three
times more than the average for the related primary catchment
Wetlands

Wetland localities
Augments the waterbodies and wetlands from the National Land Cover 2000 (Van
den Berg et al. 2008) with inland water features from Department of Land Affairs’
Chief Directorate: Surveys and Mapping (DLA-CDSM). All of these have been
classified as either ‘natural’ or ‘artificial’ wetlands to derive National Wetland Map 3.
Wetland data layers from Mpumalanga and KwaZulu-Natal provinces, and the fine-
scale biodiversity planning domains of the Cape Floristic Region have also been
added.

Wetland ecosystem types

Classifies wetlands on the basis of a hydrogeomorphic approach to Level 4a of the
national wetland classification system (SANBI 2010) using a GIS protocol for
automation. These were then combined with groupings of the vegetation map of
South Africa (Mucina and Rutherford 2006) to derive wetland ecosystem types that
were used to depict the diversity of wetland ecosystems across the country.

Wetland condition
Uses the proportion of natural land cover in and around the wetland as an indicator to
model wetland condition. For riverine wetlands, the condition of rivers was also taken
into account. Wetland condition was used to favour the selection of wetland FEPAs,
although wetlands did not have to be in a modelled good condition (similar to an A or
B ecological category; Table 3.3) to be chosen as a FEPA.
Wetland ranks
Ranks wetlands according to conservation importance using a combination of
special features and modelled wetland condition. Special features included expert
knowledge on features of conservation importance (e.g. extensive intact peat
wetlands, presence of rare plants and animals) as well as available spatial data on
the occurrence of threatened frogs and wetland-dependent birds. Wetlands of high
conservation importance were selected for representation first, proceeding to lower
ranking wetlands only if necessary.
Wetland clusters
Groups of wetlands within 1 km of each other and embedded in a relatively natural
landscape. This allows for important ecological processes such as migration of frogs
and insects between wetlands. FEPAs were identified to represent clusters in each
wetland vegetation group.

Wetlands

General info (Nel, 2011)

Approximately 45% of our remaining wetland area in South Africa is in a heavily or

critically modified condition, owing to human impacts of damming, draining and
bulldozing of wetlands. This is of immense concern given the important regulating
ecosystem services that healthy wetlands provide, such as their filtering ability, and
their role in drought mitigation and flood attenuation. The belt of heavily modified
wetlands is particularly prevalent in Gauteng, along the escarpment and in the
Western Cape province (Figure 3.15). The contribution wetlands perform to drought
mitigation and flood attenuation in these areas is likely to have eroded. This is
particularly concerning from the viewpoint of ecosystem-based adaptation to changes
in land cover and climate, as the prediction is that there will be an increase in the
frequency of droughts and storm events respectively in the Western Cape and
Gauteng provinces.

Silwerstroom area

Wetland 1
= left side polygon (red)

Cluster_ID: 66239

 Wetland that was part of a wetland cluster

NATART
= Natural
MAJNAT = 1

 Considered majority natural

Unchannelled valley-bottom wetlands on valley floors

Remaining inland wetlands on valley floors

Geomorphic type (NWCS_L4): Unchannelled valley-bottom

= A mostly flat valley-bottom wetland area without a well-defined stream channel
running through it, characterised by an absence of distinct channel banks and the
prevalence of diffuse flows, even during and after rainfall events. Water inputs are
typically, from an upstream channel, as the flow becomes dispersed, and from
adjacent slopes (if present).

 defined by Level 4a of the national wetland classification system (SANBI

(2010))

Landform type (NWCS_L3): Valley floor

An elongated, relatively narrow region of low land between ranges of mountains,
hills, or other high areas (such as sand dunes), often having a river or stream running
along the bottom

1. Canyons, deeply incised streams

Wetland condition: AB
= minimum percentage natural land cover was ≥ 75%

 considered in good conditions

Wetland rank: 5
Wetlands (excluding dams) within a sub-quaternary catchment identified by experts
at the regional review workshops as containing impacted Working for Wetland sites

Wetland 2
= right side polygon (orange)

Cluster_ID: 0

 Wetland was not part of a wetland cluster

NATART
= Artificial

Geomorphic type (NWCS_L4): Channelled valley-bottom

A mostly flat wetland area on a valley floor (see valley floor) that is dissected by
and typically elevated above a well-defined stream channel (see channel).
Dominant water inputs to these areas are typically from the channel (when it
overtops or from sub-surface discharge) and from adjacent valley-side slopes

 defined by Level 4a of the national wetland classification system (SANBI

(2010))

Landform type (NWCS_L3): Valley floor

An elongated, relatively narrow region of low land between ranges of mountains,
hills, or other high areas (such as sand dunes), often having a river or stream running
along the bottom

1. Canyons, deeply incised streams

Channelled valley-bottom wetlands on valley floors

identified by intersecting the remaining inland valley-floor wetlands with the 1:50 000
river lines (DLA-CDSM 2006).

Wetland condition: Z3
= minimum percentage natural land cover was < 25%

 Considered in heavily modified condition

Wetland rank: 6
Any other wetland (excluding dams)
Wetland 3
= right side polygon (red)

Cluster_ID: 66329

 Wetland that was part of a wetland cluster

NATART
= Artificial

Unchannelled valley-bottom wetlands on valley floors

Remaining inland wetlands on valley floors

Landform type (NWCS_L3): Valley floor

An elongated, relatively narrow region of low land between ranges of mountains,
hills, or other high areas (such as sand dunes), often having a river or stream running
along the bottom

1. Canyons, deeply incised streams

Geomorphic type (NWCS_L4): Unchannelled valley-bottom

= A mostly flat valley-bottom wetland area without a well-defined stream channel
running through it, characterised by an absence of distinct channel banks and the
prevalence of diffuse flows, even during and after rainfall events. Water inputs are
typically, from an upstream channel, as the flow becomes dispersed, and from
adjacent slopes (if present).

 defined by Level 4a of the national wetland classification system (SANBI

(2010))

Wetland condition: Z3
= minimum percentage natural land cover was < 25%

 Considered in heavily modified condition

Wetland rank: 6
Any other wetland (excluding dams)
7. STEP 4: ASSESS THE RISKS FROM PROPOSED
DEVELOPMENTS AND DEFINE MITIGATION MEASURES
NECESSARY TO PROTECT MAPPED WATER RESOURCES IN
THE STUDY AREA
By (Macfarlane, 2014)
Threats posed by lateral (diffuse) surface inputs were qualitatively assessed on the
level of threat posed by land use activities associated with each sub-sector on the
following aspects:
• Water Quantity – volumes of flow
• Water Quantity – patterns of flow
• Sedimentation and turbidity
• Water Quality – Increased inputs of nutrients
• Water Quality – Increased toxic contaminants
• Water Quality – changes in pH
• Water Quality – concentration of salts (salinization)
• Water Quality – temperature
• Water Quality – pathogens (i.e. disease-causing organisms)

Sensitivity
The sensitivity of water resources to lateral impacts is another factor that affects the
level of risk posed by a development. A more conservative approach is therefore
required where proposed developments take place adjacent to water resources
which are sensitive to lateral impacts as opposed to the same development taking
place adjacent to a water resource which is inherently less sensitive to the impacts
under consideration. For example: Agriculture, posing a high siltation threat may be
planned alongside a small and isolated depression wetland (pan) that is highly
sensitive to lateral sediment inputs. The risk posed by agricultural activities in this
instance is far
higher than for agricultural activities adjacent to a large floodplain wetland,
characterized by inherently high natural sediment inputs.
The assessment of sensitivity is based on key attributes of different water resources
that act as easily measurable indicators. The sensitivity assessment has therefore
been tailored for wetlands, rivers and estuaries.

 Silwerstroom river: 1.08 – 1.15  High to Very High

o Water resource is likely to have a high/very high susceptibility to the
specific impact type

River
Sensitivity to changes in water quantity (volumes of flow) from lateral inputs

 Affected by stream order, channel width and perenniality

 Silwerstroom river
o Order: 1
o Channel width: ~ 5 – 30m
o Perenniality: perennial/seasonal
 only flow during wet periods, drying up in dry seasons, often fed
only by rain or snowmelt
o sensitivity score: 1.15

Sensitivity to changes in patterns of flow (frequency, amplitude, direction of flow) from

lateral inputs

Wetlands

Overall sizes
Wetland size provides a broad surrogate for sensitivity to changes in water inputs.
Large wetlands have a greater inherent buffer capacity and are therefore less likely to
be affected by changes in lateral water inputs than small wetlands where moderate
changes in water inputs could have a substantial impact by affecting hydrologic
functions and reducing water available to support wetland biota.

Sensitivity to changes in water quantity (volumes of flow) from lateral inputs

Sensitivity scores
Wetland 1 & 3: 1.075
Wetland 2: 1.15

Sensitivity to changes in patterns of flow (frequency, amplitude, direction of flow) from

lateral inputs
EXCULSION MAP

In marina waters, minimise organic loading and stagnation through circulation design
and avoide enclosed basins to avoid hypoxia and algal blooms (Radke et al., 2004b).
Position marina infrastructure to maximise tidal exchange and minimise residence
time. Declare exclusion or strict-control zones in poorly flushed depositional pockets
(mud basins, inner-estuary shoals, lee of structures) where fine sediments and
nutrients accumulate (Freeman et al., 2019b).
Avoid works in or immediately upstream of existing mud basins and nursery habitats
where sediment-bound contaminants would accumulate or be resuspended (Lijklema
et al., 1993b).

Lijklema et al. 1993 — Water Quality Impacts of Sediment Pollution and the Role of
Early Diagenesis

Sediments as “Dustbins”
• Receive both natural and anthropogenic materials (e.g., phosphate, heavy
metals).
Water Quality Impacts
• Contaminant release via:
o Diffusion (important for soluble metals like Cd)
o Resuspension (important for strongly sorbed pollutants)
o Internal phosphate loading, which can sustain eutrophication even after
external loads drop.

Biological Exposure
• Sediment–water interface is habitat for algae, bacteria, eggs, zoobenthos, fish.
• Pollutants can biomagnify through food chains.
Conclusion
• Sediments are dynamic, not passive pollutant sinks.
• Early diagenesis determines long-term mobility, ecological impact, and
recovery potential.
• Proper sediment criteria and monitoring essential for management.
Nutrient Dynamics
• Strong intra-annual variability linked to agriculture:
o High NO₃⁻ in autumn–winter (fertilizer application).
o High total P in summer (point-source wastewater).
• Long-term changes:
o Nitrate concentrations ↑ 2.5×.
o Water discharge ↓ 3×.
o Net effect: ↓ nitrate flux (flow reduction dominates).

Heavy Metals
• Elevated Pb, As in dissolved phase; Pb exceeds freshwater chronic criteria.
• Stream sediments rich in Zn, Cr, Pb, As.
• Sources:
o Industrial effluents & tailings (major).
o Ophiolite weathering (natural but significant).

Karageorgis et al. 2003 — Water and Sediment Quality Assessment of the Axios
River and Its Coastal Environment

Quality Criteria Results

• Only Pb exceeds water quality criteria.
• Sediment criteria violated for As and Cr (both river and marine).
• Need to determine oxidation state (e.g., carcinogenic Cr(VI)) for toxicity
assessment.
• Nutrient increase, metal contamination, and sediment enrichment all linked to
land-use change and industrial activity.

(Karageorgis et al., 2003)

Marine sediments of the Thermaikos Gulf clearly reflect heavy-metal sources, namely
the Axios and Aliakmon Rivers as well as the city and industrial zone of Thessaloniki
Nutrient over-enrichment occurs during the low flow periods, as well as during
autumn–winter. This seasonal variability is attributed to agricultural activities, and
domestic wastewaters, which are released, untreated or partly untreated to the
river.
Overall, the water quality of Axios R. has been impacted by the anthropogenic
activities in the watershed. Increased accumulations of heavy metals such as
chromium and arsenic in the Thermaikos Gulf have been observed, and they
are directly attributed to the Axios (and Aliakmon) River loads.