Sustaining Biodiversity During Declining Water Quality

Stormwater in Western Australia

by Mikaela Hearne

Managing the quality of surface water and groundwater systems is essential for sustaining aquatic ecosystems, as well as the considerable variety of waterway types and the unique biodiversity they support within Western Australia (WA). Water quality generally refers to the physical, chemical and biological characteristics of the water and the underlying sediment. Understanding these parameters and their behaviour, is integral to managing their effects.

Within WA, the main water quality issues our waterways are facing include salinisation, eutrophication, low dissolved oxygen, acidification, erosion and sedimentation. Below is a brief discussion with regards to some current management solutions that are being implemented within WA and a case study that demonstrates how these solutions are improving the water quality within some of the state’s waterways.

So why is our water quality in decline?

A range of factors impact our local water quality here in WA and the overall ecological health of our waterways and include:

  • Excess nutrients (phosphorus and nitrogen) and organic loading enter the river systems (particularly the Swan Canning System and Peel-Harvey Inlet) through groundwater, drainage and catchment run-off;
  • Contaminants – such as heavy metals, hydrocarbons, pesticides and herbicides enter the waterways through drainage networks and can have a toxic impact on organisms, aquatic lifecycles and food chains (DPAW, 2020);
  • Acid Sulfate Soils that are disturbed during construction and excavation works, can lead to non-nutrient contaminants and acidification of waterways;
  • Climate change, including rainfall, temperatures, evaporation and extreme weather events influence our local water cycle, which is a primary driver of the hydrology of waterways; and,
  • Changes in land use, excess clearing of vegetation and changing weather patterns affect the flows between groundwater and surface water and the amount of salt they contain (DWER, 2020).

The Effects

The factors mentioned above are by no means an extensive list, however these are the main drivers to declining water quality within the Perth Region.

So, let’s take a closer look at the current impacts of each of these aspects.


Eutrophication is nutrient enrichment and it drives an excess in primary productivity within our waterways. Human interference alters the way which water flows off the natural landscape, when the land use changes and vegetation is stripped, for agriculture or urban developments the natural drainage is altered and there can be insufficient vegetation surrounding rivers and estuaries (riparian vegetation) to utilize and filter the excess nutrients. Additionally, the nutrients added to the landscape through fertilisers, pesticides and animal manure contribute to nutrient enrichment in some surface water bodies. High concentrations of nutrients may encourage algal blooms, which eventually collapse and decompose which in turn depletes the oxygen from the water that then ultimately places stress on aquatic life and can lead to fish kills (DWER, 2020).

Algal and Cyanobacteria Blooms

Algal blooms are a natural phenomenon; however, their increased frequency and intensity leads to the loss of biological function of wetlands, rivers, estuaries and oceans. In extreme cases macroalgal and microalgal growth can dominate an estuary system, such as what happened in the Peel Harvey inlet during the late 1980’s.  During the early 1990’s, the toxic species of phytoplankton Nodularia Spumigena replaced the macroalgae that had smothered the seagrasses and their domination took over to cause ecosystem collapse (DWER, 2020). These blooms of microalgae, macroalgae, dinoflagellates (red tides), cyanobacteria (blue-green algae) and phytoplankton are harmful when they produce toxins that adversely affect aquatic life (particularly shellfish) and human health (through swimming and consumption of shellfish) and when in vast quantities, they cover seagrass communities, which leads to the loss and decline of an important marine habitat and biodiversity.


Salinity can come in the form of primary (natural), secondary (dryland) and tertiary salinity (irrigation salinity). Small amounts of dissolved salts in the natural water is vital for the life of aquatic plants and animals; higher levels of salinity alter the way the water can be used and salinisation of streams and rivers can threaten ecosystems and their constituent species. Many plants tolerate higher salinities for short periods but cannot also survive long periods of inundation (Barrett-Lennard EG, 2003).

Acid Sulfate Soils

Acid sulphate soil is a name given to soils or sediments containing iron sulphides. When disturbed by drainage, lowering of water-tables or excavation, oxidation of the sulphides creates sulphuric acid which can trigger a range of flow-on effects, including acidification of groundwater, wetlands and waterways, leaching of aluminium, iron, manganese and arsenic from the soil matrix into wetlands, rivers and estuaries and the formation of black muds (monosulphidic black ooze) (MBO) that rapidly deoxygenate the water and can lead to fish kills (DWER, 2020). MBO has been an environmental concern within the Peel – Harvey system for many years.

Fish Kill events

Fish Kills can occur during natural events; however, they are also an indicator of poor water quality (salinity, pH, turbidity, TDS and temperature). Low dissolved oxygen through decay of algal blooms and other organic matter, contaminants such as hydrogen sulphide, carbon dioxide, ammonia, methane, metals and algal toxins can all lead to localized fish kills (DWER, 2020).

Flow regimes and aquatic connectivity

The health of the waterways is a complex balance between the hydrology and the interactions between bacteria, algae, plants, animals, sediments, water flow, groundwater and chemicals. Reduced rainfall causes less frequent flows in waterways affecting flora and fauna and the groundwater recharge, which adversely affects the groundwater dependent ecosystems it supports. Some species need permanent water and others naturally adapt to periods of low to no flow (DWER, 2020).

Water temperature affects the distribution of aquatic organisms and can cause localized extinction of some vulnerable species (DWER, 2020). Temperature changes can affect some species ability to assess breeding cues, which leaves insufficient time to complete their life cycles. As temperatures rise, evaporation increases and rainfall declines, some wetlands completely disappear and aquatic organisms lose their vital habitat and the connectivity of water bodies, meaning aquatic species cannot disperse or migrate as needed for food, shelter from predators, spawning/breeding purposes and migration to nursery areas.

The connectivity to a section of waterway (river, estuary) to its floodplain and to the upstream and downstream sections influences sediment and nutrient movement and henceforth is vital for a healthy waterway. The floodplains offer an important habitat for fish, crayfish, frogs and wading birds. Seasonal flooding to these areas is crucial for a stage of their life – cycle. Reproduction of some species is adversely affected, for instance tadpoles may not have time to develop into frogs before their habitat dries out (DWER, 2020). Many native fish species move into the floodplains and annual creeks during winter periods to reproduce in the flooded vegetation (Morgan et al 1998). Juvenile fish develop within these nursery habitats prior to moving into the more permanent waterways.

As sea levels rise due to melting ice, low-lying coastal freshwater floodplain and wetland ecosystems are at risk as inundation events increase and vegetation has less time to recover following more consistent and regular flooding by seawater (DWER, 2020).

Estuaries are affected by increasing marine influence and changing habitat distribution and quality. These systems are also influenced by an increase in saline habitats, altered sand bar dynamics, shoreline erosion and sediment redistribution and changes to stratification within the water column. South-west estuaries are more likely to experience reduced flushing of sediments, nutrients and pollutants as they are affected by both sea level rise and reduced river flows (DWER, 2020).

Solutions to improving water quality

Several feasible solutions have been implemented throughout the state in order to manage our waterways and ensure the water quality remains intact and ensure biodiversity is maintained.

Water Sensitive Urban Design

Water sensitive urban design (WSUD) is one such solution, which offers an alternative to more traditional approaches in stormwater management. By integrating flow paths in the landscape and adopting water sensitive design strategies and technologies, such as detention and retention basins, grassed swales and vegetation to facilitate water infiltration and pollutant filtration an integrated approach to stormwater management can be adopted and stormwater can become a resource rather than a nuisance and potential carrier of pollutants adding to poor water quality (CSIRO, 2006).

The urban water cycle should be managed as a single system, which all urban water flows are recognised as a potential resource where interconnectedness of water supply, groundwater, stormwater, wastewater, flooding, water quality, wetlands, watercourses, estuaries and coastal waters is present.

WSUD aims to manage water quality of surface water through; managing runoff from rainfall events in high catchment areas; minimising hydrological changes at critical internal and final discharge points of the stormwater system. The general objectives of WSUD as per the Stormwater Management Manual for WA, (2004-2007) are to manage the water regime through.

  • Maintaining appropriate aquifer levels, recharge and surface water characteristics in accordance with assigned beneficial uses;
  • Managing groundwater recharge sustainably;
  • Preventing flood damage in developed areas; and
  • Preventing excessive erosion of waterways, slopes and banks.
  • Maintaining and where possible enhancing water quality
  • Minimising waterborne sediment loading;
  • Protecting riparian vegetation and natural landscape;
  • Protecting and restoring wetlands and waterways health
  • Minimising the export of pollutants such as phosphorus and nitrogen to surface or groundwater;
  • Preventing groundwater acidification processes; and
  • Minimising the export and impact of pollution from sewerage.

Several techniques are used in WSUD and some of these, which contribute to the enhancement and protection of water quality and natural flows and therefore sustain biodiversity, some of which are discussed in further detail below.


Biofiltration systems are excavated basins or trenches that are filled with porous filter media and planted with vegetation to remove pollutants from stormwater. They use both natural and physical processes to treat stormwater and they are very flexible in their design to accommodate climate, soil and groundwater requirements.

The benefit of this design is that they can be used on large to small scales i.e. designs such as linear, basins, tree pits and planter boxes allows them to fit into different locations and they require less space to other filtration systems due to their higher infiltration rates. The pollutants that this design targets include coarse sediment, suspended solids, phosphorus, nitrogen and heavy metals (DWER, 2011).

Constructed Wetlands for stormwater management

Constructed wetlands are extensively vegetated water bodies that use sedimentation, filtration and biological uptake processes to remove pollutants from stormwater. Generally, they are not deemed suitable where contaminated or nutrient rich groundwater is intercepted. The large detention volumes required to accommodate this design, require larger areas of land, so they are not always feasible for all urban projects. A good example of a constructed wetland in the Perth Region, is the Point Fraser constructed wetland in East Perth which reclaimed some of the previous wetland area from prior to Perth City development. The pollutants that this design targets include coarse sediment, suspended solids, phosphorus, nitrogen and heavy metals (DWER, 2011).

Dry or ephemeral detention areas

A dry or ephemeral detention area is a depression that temporarily holds stormwater and releases it at a slower rate than it comes in. This design reduces the downstream flow rates and decreases flow velocities to prevent downstream erosion and flooding. They work to improve the quality of stormwater by allowing sedimentation of particle-based contaminants. The lowest point is located above the maximum groundwater level and they drain following each stormwater event to prevent full storage volumes, hence the term ‘dry or ephemeral’ (DWER, 2011). This design targets litter, coarse sediment and suspended solids.

Infiltration basins and trenches

This design is aimed at capturing and storing stormwater prior to it reaching the soil profile. These basins and trenches can maintain site water balance and can replenish local groundwater. These designs are simple to construct, are easy to maintain and work well in sandy soils. The pollutants that this design targets include litter and organic matter, coarse sediment, suspended solids, phosphorus, nitrogen and heavy metals (DWER, 2011).

Living streams

A living stream is a constructed stormwater conveyance channel that mimics the morphology and vegetation of natural streams. Additionally, this design treats the stormwater using physical and biological processes and create diverse habitat for wildlife. These living streams can become complex ecosystems supporting a wide range of flora and fauna, and essentially restore and sustain biodiversity within an area (DWER, 2011).

Case study – Peel Harvey WSUD

A management strategy for the Peel Inlet and Harvey Estuary System was approved for implementation by the Minister for the Environment on 4 July 1989 (EPA, 2003). The Peel-Harvey system was susceptible to massive micro and macro algal growth (including blue-green and potentially toxic dinoflagellates) due to increase in nutrients, especially phosphorus from the estuaries coastal catchment (EPA, 2003). The Construction of the Dawesville channel was a one major thrust designed to allow the system to become “visibly clean and healthy and ecologically healthy and resilient’ (EPA, 2003). The other thrust was the implementation of an integrated catchment plan. Although the system has improved a lot since the installation of the Channel, the ecosystem is still in a fragile condition due to ongoing population growth, intensity of catchment use and climate change (Rogers, Hall, Valesini, 2010). The lower reaches of the system, including the Serpentine and the Murray and Harvey rivers are still in a perilous biological state (Rogers et al; 2010). The health of water ways in the Peel-Harvey Inlet are relied upon by many water birds, fish and macroinvertebrates, all of which have seen a decline in growth, health and population during pollution events over the years.

In 2003, the Australian Government’s Coastal Catchment Initiative identified Peel-Harvey Inlet as a priority hotspot. Along with several other management and monitoring strategies for the system, WSUD has been identified as the most beneficial and holistic management approach for this water system pertaining to urban catchment areas. It aims to address the water quality, water quantity and water conservation, together with broader social and environmental objectives within the context of urban planning and development. Within the Peel-Harvey catchment there are 10 sites, that showcase different methods of achieving better urban water management outcomes. Each site includes a response tailored to the specific conditions and constraints.

This article will briefly outline three of the ten sites; Site 4 – Channel View, Dawesville; Site 6 – Snake Drain, Mariners Cove and; Site 7 – Alcoa Pinjarra Wetland, Pinjarra Road.

Channel View, Dawesville

This site has been built on an area sensitive to nutrient loading and contamination discharge. In order to prevent further negative environmental impacts in the area, special attention was given to the implementation of water sensitive urban design principles, particularly to prevent nutrients from mobilising to the nearby estuary (New Water Ways, 2020). The design uses a bioretention system with rockfall to slow and treat frequent stormwater events prior to discharge to receiving environment including the estuary. The site also incorporates soak tanks and grassed swale areas to increase infiltration onsite. A key objective of this site is there be ‘no direct discharge of stormwater into the estuary’ (New Water Ways, 2020).

Snake Drain, Mariners Cove

The snake drain is located on the edge of the internationally significant Creery Wetlands, a key component of the Ramsar listed Peel-Yalgorup System. The protection of these wetlands, having consideration of the shallow depth to groundwater and predominantly clay soils were key elements guiding the design of this area (New Water Ways, 2020). This site utilises gross pollutant traps to prevent litter and other pollution from entering the wetlands, lineal swale to retain and convey stormwater by allowing for nutrient assimilation, a constructed lake to retain and treat stormwater and retention native vegetation to protect the health of nearby Ramsar wetlands (New Water Ways, 2020).

Alcoa Pinjarra Wetland Restoration

Formerly a wetland, this degraded reserve had been filled and channelized to form an urban drain. This site was chosen based on many factors including that it conveys more than 20% of the Pinjarra town site stormwater which is discharged directly into the Murray River approximately 500m downstream. The site also had significant remnant vegetation and an indigenous cultural history, and due to the size of the reserve there was room to undertake a large-scale intervention. The project reinstated the former wetland functions of the site; assisting with nutrient stripping through encouraging sedimentation and nutrient uptake by native sedges, rushes, shrubs and trees planted on the banks. An important design specification of the project was to maintain the conveyance capacity in high flows while slowing down the water in low flow periods (New Water Ways, 2020). The Murray River is subject to algal blooms, so pollution and nutrient control through urban design of stormwater management can assist with reducing nutrient loading, eutrophication and algal blooms.

Summarising Thoughts

Since water quality is of vital importance to sustaining biodiversity, it is imperative that continued monitoring of our water systems and proper urban management through water sensitive design is carried out across the state and particularly in these systems most susceptible to the impacts discussed in this article. With a region that relies heavily on our waterways for recreation, community belonging, cultural heritage, tourism, health, food resources and drinking water, going forward developments and urban areas must consider their potential environmental impacts, alterations to vegetation, drainage, nutrient and non-nutrient contamination flows. As a final thought, the emerging and ever relevant issue of climate change poses possibly the greatest environmental threat likely to impact Western Australia’s waterways, including the Peel Harvey Estuary and its nearby coastline during this century.

Resources and References

Peter Rogers, Norm Halls, Fiona Valesini, Science Strategy for the Peel Harvey Estuary, July 2010 –

Peel Inlet and Harvey Estuary System Management Strategy: Progress and Compliance by the Proponents with the Environmental Conditions set by the Minister for the Environment in 1989, 1991 and 1993 –; EPA, January 2003.

Department of Water, Waterways and Wetlands, Perth-Peel regional water plan background paper, September 2009

Barrett-Lennard EG 2003 ‘The interaction between waterlogging and salinity in higher plants: causes, consequences and implications’. Plant and Soil Vol 253, pp 35-54