Coastal waterways

Coastal waterways are the arteries of coasts, providing key habitats for aquatic species, transporting food and nutrients, and flushing waste. For the purposes of this report, the Coasts chapter covers waterways within the headlands of estuaries and bays. Waters outside the headland are discussed in the Marine chapter (see the Marine chapter) and waters that flow into coastal waterways from further inland are discussed in the Inland water chapter (see the Inland water chapter).

Australia’s coastal waterways vary widely in size and shape, ranging from tide-dominated estuaries in the north and far south of the country to wave-dominated estuaries more common in New South Wales, South Australia, Victoria and Western Australia (Heap et al. 2001). There are also coastal lakes and lagoons, tidal creeks, wave- and tide-dominated deltas, and stranded plains (Heap et al. 2001), all with unique traits that provide habitat for native flora and fauna.

Many coastal waterways are attractive, productive and relatively sheltered, but these qualities also mean they are heavily used and exploited by humans. Some are the focal point of cities or regional centres, and are consequently exposed to numerous pressures from recreation, industry and trade (Hallett et al. 2016b). In general, the condition of coastal waterways depends on their proximity to population, agriculture and industry, but a lack of long-term monitoring and inconsistent monitoring approaches limit our understanding of changes in their condition through time or space.

For coastal Indigenous peoples, waterways that run through sea Country are a focal point for many activities including leisure and obtaining food (Stronach et al. 2019). Being highly productive environments, these habitats play an important part in the education and the knowledge-sharing aspects of the lives of coastal Indigenous people, connecting them to Country and continuing lore. Connections to these waterways are observed through many artworks, dances, stories, customs and ceremonies (see the Indigenous chapter).

Assessment The condition of coastal waterways
2021 Assessment graphic showing the environment is in poor condition, resulting in diminished environmental values, and the situation is stable.
Limited confidence
Indigenous assessment
2021 Assessment graphic for an assessment conducted by Indigenous community members, showing the environment is in poor condition, resulting in diminished environmental values, but the trend is unclear.

Coastal waterways vary in their exposure to human impacts and therefore their condition, but are generally in poor but stable condition nationally. Water quality is, however, considered good. The condition of estuaries and bays, and water quality have been relatively stable in recent years, but the trend in coastal lakes and lagoons is unclear due to lack of monitoring. The Indigenous assessments for the state of waterways found that 2 assets are poor and 1 is good, and the trend is stable for 1 asset and unclear for 2. Local government assessments (see Approach) indicate that waterways near major capital cities are considered to be in poor condition, while those outside those areas are generally regarded as good. Related to United Nations Sustainable Development Goal target 14.2

Assessment Estuaries and bays
2021 Assessment graphic showing the environment is in poor condition, resulting in diminished environmental values, and the situation is stable.
Adequate confidence
Assessment graphic from 2011 or 2016 showing the environment was in poor condition, resulting in diminished environmental values, and the situation was stable.

Many estuaries in Australia are negatively impacted by human activities and climate change. The Indigenous assessment for some regional areas was poor, with a stable trend.

Assessment Water quality
2021 Assessment graphic showing the environment is in good condition, resulting in stable environmental values, and the situation is stable.
Limited confidence

Water quality is moderately good in coastal Australia. The trend is stable, but issues such as climate extremes and coastal development remain a concern. The Indigenous assessment for some regional areas was good, with an unclear trend.

Assessment Coastal lakes and lagoons
2021 Assessment graphic showing the environment is in poor condition, resulting in diminished environmental values, but the trend is unclear.
Low confidence
Assessment graphic from 2011 or 2016 showing the environment was in poor condition, resulting in diminished environmental values, and the situation was deteriorating.

Human activities are degrading habitats and habitat quality, but data are poor and geographically variable, rendering the current state and trend uncertain. The Indigenous assessment for some regional areas was poor, with an unclear trend.

Estuaries and bays

Estuaries and their surrounding wetlands are bodies of water found where rivers meet the sea, forming the interface between freshwater and marine waters. Bays are moderately sized inlets of the coast and are dominated by marine waters.

These environments contain a variety of habitats, including seagrasses, mangroves, shellfish reefs and rocky reefs, and a variety of sediment types. This diversity of habitats, and for estuaries their variable physicochemical environment, means that these systems support a unique and abundant mix of species and assemblages (collections of species). Due to their high productivity, these environments are significant coastal areas for Indigenous peoples for both cultural heritage and continuation of cultural practices.

Overall, estuaries near urban areas remain in poor condition, although there is considerable variability among individual systems. This is despite many initiatives to reduce nutrient run-off and undertake remediation and restoration in the catchments, and advances in estuarine modelling to help inform management decisions.

Into the future, estuaries and bays are likely to be under increasing pressure due to growing human population and the impacts of climate change.

Condition of estuaries and bays

As sheltered and productive environments, estuaries and bays are focal points for human populations and are often heavily developed and utilised. Humans have also modified estuary catchments, such as through land clearing and intensive agriculture.

Due to their dynamic physicochemical environments, some estuaries are regarded as ‘naturally stressed’ (Elliott & Quintino 2007) as their levels of oxygen, temperature and salinity can vary widely and change rapidly. These natural stresses can then be exacerbated by human influences, such as excess nutrients (eutrophication) coming from agricultural run-off.

Microtidal estuaries (i.e. those with a tidal range of less than 2 metres; (Tweedley et al. 2016)), and especially those with intermittently closed entrances such as those in south-western Australia, are particularly vulnerable to human perturbations and climate change (Hallett et al. 2018, Warwick et al. 2018). This is because their long water-residence times facilitate the accumulation of contaminants and promote algal blooms and stratification, which can lead to hypoxia and anoxia. In Mediterranean and arid climates, high temperatures and low or seasonal rainfall can result in marked hypersalinity, resulting in loss of species, ecosystem complexity and probably function (Warwick et al. 2018, Krispyn et al. 2021).

For estuaries that become intermittently closed from the ocean by the formation of a sandbar, changes in freshwater discharge can result in either freshening or hypersalinity, leading to mass mortalities of fish (Hoeksema et al. 2018, Tweedley et al. 2019, Scanes et al. 2020a). Notable examples include salinities of up to 313 parts per thousand (ppt) in Culham Inlet and 345 ppt in Hamersley Inlet, both in south-western Australia (Figure 9). Hamersley Inlet experienced a bloom of red microalgae after low rainfall and prolonged closure from the ocean in November 2020. The once-natural cycle of temporary closure to the ocean (Scanes et al. 2020b) has been exacerbated by extraction of water from estuarine catchments, and the situation is likely to become worse with climate change.

Estuary and bay management

Estuary and bay systems require active and novel management driven by robust and coordinated monitoring and evaluation programs, as well as cooperation between various management agencies and policy-makers. Entrance management (e.g. training walls, dredging and artificial breaching) can modify physicochemical conditions and sediment transport, and thereby influence the type and quality of habitats that estuaries sustain.

There are a plethora of catchment-level management programs, but many are long-term programs and yet to yield significant change. Ideally, management approaches should mitigate pressures at the source. However, this is not always possible in the short term, particularly for nonpoint-source issues such as eutrophication, for which whole-of-catchment approaches may be required. For example, improved fertiliser management programs and restoration of riverine riparian vegetation can reduce eutrophication, but must be applied catchment-wide and take time to implement.

Although the restoration of estuarine and coastal environments is a relatively new field (Saunders et al. 2020), efforts are underway to restore estuarine seagrass and shellfish habitats (Fitzsimons et al. 2020, Tan et al. 2020). Shellfish reefs with current restoration projects include Port Stephens (New South Wales), Pumicestone Passage (Queensland), Gulf St Vincent (South Australia), Port Phillip Bay (Victoria) and the Swan-Canning Estuary (Western Australia). There is emerging evidence of success in oyster reef restoration (Gilby et al. 2021), which – if continued and scaled up – could improve the condition of some estuaries and bays. ‘Operation Posidonia’ is an example of citizen-scientist-driven seagrass restoration in New South Wales, with promising outcomes (Ferretto et al. 2021).

There is still a need to assess, monitor and report estuarine condition in a manner that facilitates robust analysis of trends and comparisons among states, using abiotic and biotic measures of ecological processes and function (Hallett et al. 2016b). An example of this is the fish community index, which has assessed the condition of the Swan-Canning Estuary annually since 2012 (Hallett et al. 2019).

Figure 9 Hamersley Inlet, southern coast of Western Australia

Water quality

Water quality refers to the physicochemical properties of water, including temperature, salinity, turbidity, oxygen saturation, dissolved organic matter and chlorophyll-a. Good water quality is fundamentally important to help underpin healthy aquatic ecosystems; thus, water pollution from sediment or run-off in both urban and rural areas is considered a primary threat.

Coastal water quality is highly variable across space and time and is strongly influenced by local conditions (e.g. tide, weather) and climate. This means that reference conditions are regionally specific, and water quality status and trend are assessed through indices, not absolute values.

Human activities that alter coastal water quality include catchment and estuary entrance modification, agriculture, urbanisation, and dredging. There are also impacts associated with high tourism and boating traffic in some popular waterways; anecdotal evidence suggests that these impacts have changed with different patterns in tourism activities during the COVID-19 pandemic.

Climate change is a significant pressure on estuaries nationally, with warming, acidification and changes in salinity occurring at rates faster than in adjacent marine waters (Scanes et al. 2020a). Sea level rise caused by climate change will shift the position of the intertidal area of estuarine shorelines, which will alter the structure and function of intertidal ecosystems that can influence estuarine water quality. Unseasonal summer rainfall, tropical storms and bushfires can cause rapid and widespread changes in water quality by altering the physicochemical properties of estuaries through the delivery of nutrients and organic matter. These changes then have cascading impacts on ecosystem structure and function.

Catastrophic events, such as the bushfires in eastern Australia that burned more than 8 million hectares of forest during 2019–20 (DAWE 2021a), closely followed by floods, have the potential to cause significant erosion and introduction of organic carbon (i.e. topsoil, sediments, char and ash) and other materials into coastal waters, with poorly understood effects on water quality.

Generally, water quality in estuaries nationally shows a pattern of poor condition in the upstream portion where there is low tidal flushing, with improved condition towards the coast where there is greater mixing and exchange with the ocean. Natural variability in water quality in northern Australia is relatively high, which reflects the climatic and tidal regimes in the region (Fortune & Mauraud 2015). Water quality remains very good for much of the coast, but increasing pressures (e.g. population growth and economic activity (Jackson & Rankin 2017)) in populated ports have prompted the development of long-term monitoring efforts for the detection of trends. In southern Australia, riverflows have declined significantly in the past 15 years, altering flow regimes and the frequency of mouth openings, pushing salt water further upstream and worsening water quality in riverine portions of estuaries. In some systems, water stratification results in periodic to fairly constant low oxygen, periodic algal blooms and occasional fish kills.

Urban areas are also subject to a plethora of emerging issues that have potential environmental and ecological implications; however, little is known about their impacts and the issues are largely unmanaged. These issues include increased concentrations of contaminants of emerging concern, (e.g. pharmaceuticals and antimicrobials, microplastics) that are not fully removed in the wastewater treatment process, and are present in sewage leaks and wet weather overflows.

Recognition of the importance of addressing water quality issues has increased. This is reflected in plans for future coastal waterway management projects, including regulation of the impacts of point sources, pathogens, sediment and nutrient run-off. Activities include stock exclusion from streams, rehabilitation of riparian vegetation, improved effluent management on dairy farms and rectification of sewage intrusions into urban stormwater systems. In some areas, management actions have already led to improvements in water quality (e.g. broadscale environmental monitoring programs associated with salmonid aquaculture in Tasmania; (Ross et al. 2019)). Other management actions include undertaking audits, remediating existing stormwater assets and investing in alternative approaches to improve stormwater management infrastructure (Sydney Water 2022). Shellfish reef restoration, which is being scaled up nationally, will also improve water quality as these filter-feeding organisms remove particulate matter from the water column.

Across Australia, management and monitoring efforts are focused on the estuaries that are under greatest pressure (i.e. closest to population centres), and a large proportion of estuaries in some regions are unmonitored. Baseline assessments such as the Victorian Index of Estuary Condition (Arundel et al. 2009) and the New South Wales Estuary Health Program (Hallett et al. 2016a) were developed to provide consistent and systematic measurement of estuarine condition and help guide management investment. Results from monitoring can be used to inform management priorities to reduce pressures, such as occurs within the New South Wales Marine Estate Management Strategy.

In parts of Australia, industry and citizen science programs are playing important roles in contributing water quality monitoring data (see Citizen science). Citizen science grants funded through the Queensland Reef Water Quality Program are involving the community in science projects. One of the projects is led by Central Queensland University. It uses community volunteers to collect seagrass flowers from seagrass banks off Gladstone, Bundaberg and the Sunshine Coast for use in seagrass restoration. In the Northern Territory, industry contributes to an offset program, which aims to improve integrated monitoring efforts in the region.

In the Great Barrier Reef catchment, the Traditional Owner Healthy Water Grants Program is building capabilities, increasing skills and training opportunities, and strengthening partnerships to undertake healthy water projects. Additionally, 5 regional report card partnerships within the catchment (all of which are partly funded by the Australian and Queensland governments) monitor and report on estuarine and coastal ecosystem health annually, using metrics linked to water quality, habitat condition and other factors (e.g. sediment quality, environmental flows and river connectivity). In some cases, industry partners associated with these partnerships contribute their own monitoring data to the report card assessment.

Coastal lakes and lagoons

Coastal lakes and lagoons (CL&Ls) are permanent and semipermanent water bodies that are influenced by tides but not permanently connected to the ocean. CL&Ls comprise intermittently closed and open lakes and lagoons, extreme upstream areas of estuaries isolated by barriers (e.g. rock and sandbars), and brackish lagoons on tidal flats. They may be natural or formed by human construction of barriers (bund walls, weirs, roads, road culverts, canal developments, dams, and so on) (Waltham & Connolly 2013).

CL&Ls provide habitats for specialised coastal marine species, including nursery grounds for fishes, and feeding, breeding and refuge areas for water and wading birds. Their location makes them readily available to a large part of Australia’s population, so they provide important social, cultural and economic values. Disconnection and reconnection of CL&Ls to the ocean is influenced by tides, freshwater flows, waves and in some cases human activities. The combination of connection pattern, depth, local geochemistry and human influences determines the physical condition of CL&Ls, and their variability over time.

Pressures on coastal lakes and lagoons

The health of CL&Ls largely depends on the extent of urban and agricultural activity in their catchments. CL&L systems naturally vary in connectivity with the ocean, from mostly closed to mostly open (Haines et al. 2006); those that are mostly closed are more sensitive to declining water quality associated with introduction of nutrients and pollutants from the surrounding catchment. CL&Ls in Tasmania (Saunders 2011) and remote areas of northern Australia (Sheaves et al. 2014, Finlayson 2018) are often in good condition, while those in more developed areas are more highly modified. Some CL&Ls that have high conservation value, such as South Australia’s Coorong, Lower Lakes and Murray Mouth, suffer ongoing effects of drought and water abstraction, requiring ongoing efforts to ensure connectivity between the river and ocean (Kingsford et al. 2011).

Human-imposed barriers are common and may increase the area of CL&Ls available to birds and marine organisms. However, these barriers also alter connectivity to the marine environment, which may disrupt the necessary movements of organisms, alter natural water quality and promote the growth of waterweeds (Sheaves et al. 2007, Abbott et al. 2020). Barriers also modify the frequency and extent of freshwater inflow, which can alter salinity and water levels, disrupting natural ecological processes.

Additional pressures include the entry of sediment, nutrients and chemicals from catchments and nearby urban areas, altered groundwater tables, disturbance and pollution from human use (e.g. boating) (Webster & Harris 2004), and invasion by non-native organisms (see Biological pressures).

Management of coastal lakes and lagoons

The future of CL&Ls as productive ecosystems requires coordination across multiple management jurisdictions to enable whole-of-catchment management of human activities, effective and timely responses to climate change, effective scaling up of restoration activities, and long-term monitoring and assessment.

One of the key strategies used to alleviate issues of flooding and deteriorating water quality in closed CL&Ls has been artificial entrance opening (i.e. dredging). While such strategies may succeed in alleviating these issues, they lead to a state change – transitioning the system from non- or weakly tidal to tidal, and from disconnected to connected with the ocean. This may have major ecological implications such as increased biological invasion (Garside et al. 2014) and ‘genetic swamping’(where local genotypes are replaced by hybrids) (Roberts et al. 2010b).

Restoration and mitigation measures are usually small in scale and localised, and often ineffective because of a paucity of general and location-specific scientific knowledge of ecological processes. This limits effective goal-setting and the implementation of processes to monitor and ensure success (Saunders & Taffs 2009). Outcomes are also often compromised because ancillary actions needed to underpin success (e.g. riparian management) are not undertaken, usually due to legislative complexities or limited funding, or because necessary management interventions have unfavourable social consequences (Kingsford et al. 2011).