Coastal waterways


Australia has a wide variety of coastal waterways. These include tidal creeks (35 per cent), wave-dominated estuaries (17 per cent), tide-dominated estuaries (11 per cent), wave-dominated deltas (10 per cent), tide-dominated deltas (9 per cent) and strand plains (5 per cent), with the remaining 13 per cent comprising drowned river valleys, bays, coastal lakes, lagoons and creeks (Heap et al. 2001). These proportions are not consistent around the country, with tide-dominated estuaries more common in the north and far south, and wave-dominated estuaries more common in New South Wales, Victoria, South Australia and Western Australia.

Coastal lakes and lagoons

Many of Australia’s coastal freshwater resources are intermittently closed and open lakes and lagoons (ICOLLs). The majority are situated in either the south-east or south-west of the mainland, but they also occur throughout the east coast and Tasmania (Timms 1982). The most likely trend in the state of lagoons nationally is declining quality for catchments with significant human use, but a robust assessment is hindered by a deficiency in baseline data (Saunders & Taffs 2009). Large-scale spatiotemporal monitoring would be required to detect trends in the context of the cyclic ICOLL dynamics, which naturally alternate between open and closed, and affect water characteristics. Freshwater lakes are discussed in the Inland water report.

Key pressures on lagoons are the input of sediment and nutrients from the catchment, and the alteration of entrance dynamics (Everett et al. 2007). Some lagoons are permanently artificially opened, at greater frequencies or at different times than would occur naturally, and this causes rapid changes in water level, salinity and tidal regime. Modifications to entrance dynamics have biological impacts, such as increased colonisation by introduced species, and hybridisation between estuarine and marine species. Lagoon entrances are restricted when open, and often only a small amount of water is exchanged, making them particularly vulnerable to eutrophication and pollution. Entrance opening has little effect on pollution, but may help manage flooding of margins. Lagoons are also subject to pressures of recreational use, fishing, coastal development and catchment modification (Webster & Harris 2004).

Recent work in northern New South Wales and Queensland indicates that enhanced nutrient input has contributed to water quality decline (Logan & Taffs 2013). The Coorong, Lower Lakes and Murray Mouths system suffered severe deterioration following extended drought and upstream water abstraction (Haynes et al. 2007, Kingsford et al. 2011). Tasmania’s lagoons are in much better condition than other states because development pressures are lower (Saunders & Taffs 2009).

Restoration and mitigation measures are rare, apart from small-scale projects that lack the long-term funding required to sustain results. Multistakeholder agreements on water abstraction to restore environmental flows have the potential to improve water quality in coastal lakes and lagoons such as the Coorong. Smaller-scale restoration projects may be unsuccessful because of poor knowledge of the characteristics of specific lagoons and multiple interacting pressures. Understanding and conserving lagoons require studies beyond specific taxonomic groups, and better understanding of ecological processes.

The outlook for lagoons will be tightly coupled with human population growth, and the associated modification of catchments and lagoon entrances. Unless appropriate management actions are taken, ongoing deterioration of lagoons is predicted from poor development and land-use decisions, water abstraction upstream, introduced species, nutrient inputs and saltwater intrusion. The longer-term outlook also depends on the effects of climate change on entrance dynamics.

Estuaries and bays

As productive, aesthetically attractive and relatively sheltered features of the coast, many estuaries and bays are heavily used by humans for recreation, industry and trade. Some estuaries and bays support large and growing urban centres, and are consequently exposed to multiple pressures (Hallett et al. 2016a). The condition of estuaries and bays largely depends on their proximity to population, agriculture and industry, but lack of long-term monitoring and the variability in approach for assessing estuarine condition limit the ability to make national or state-level assessments about their condition (Hallett et al. 2016d).

In the short term, modified estuaries and bays may not experience significant change because they are already severely altered. These areas may improve as legacy contamination issues are slowly addressed and contamination inputs (both point source and diffuse) are reduced. Bays and estuaries are targeted in marine estate planning aimed at addressing local pressures such as agricultural run-off and unsustainable fishing, but there is insufficient evidence that current habitat restoration efforts are effective, and protection needs to be applied on appropriately large spatiotemporal scales to restore functioning. In the long term, climate change (particularly sea level rise) and urbanisation are likely to continue to affect estuaries and bays. For example, sea level rise threatens urbanised estuaries with little remaining opportunity for habitat retreat (see Sea level rise). However, positive outlooks exist where improvements in management planning frameworks are under way or planned to help mitigate impacts (Koss et al. 2015). For example, although carbon dioxide enrichment increases the probability of biogenic habitat loss, there is evidence that this loss can be managed by reducing eutrophication.


Estuaries are embayments where there is a transition zone between a freshwater river and the ocean. A range of ecologically important habitats and habitat-forming species are found within estuaries, including mangroves, seagrasses, oyster reefs, rocky reefs, soft sediments and beaches. Estuaries are home to a diverse suite of species, even when extensively modified (Clark et al. 2015). In this report, we cover areas within the heads of estuaries, but note that the freshwater influence of some estuaries can extend far offshore at times of high flow. This is the case for some tropical river estuaries, where discharge plumes can reach the continental shelf during strong flow conditions, and thereby influence offshore habitats covered in the Marine environment report.

The condition of estuaries and their outlook vary widely around Australia (Wolanski 2014). Approximately half of Australia’s estuaries are significantly modified by coastal development and human activities, a large proportion of which are in the temperate south. Tropical estuaries in the north typically differ from temperate estuaries in their physical characteristics (e.g. they are generally high turbidity and experience periodic high flow), and most are relatively pristine.

A recent survey of 10 New South Wales estuaries found some of the highest sediment metal concentrations anywhere in the world, particularly in Sydney and Port Kembla harbours (Dafforn et al. 2012). Despite this, fish (McKinley et al. 2011b), infauna (Dafforn et al. 2013) and hard-substrate epifauna (Clark et al. 2015) were abundant and diverse. This pattern is likely because nutrient enrichment is increasing the total biomass of organisms, and high vessel activity is introducing new species. Therefore, although some modified estuaries support productive and diverse ecosystems, they are significantly altered from their natural state (Clark et al. 2015).

In South Australia, the amount of rural run-off delivering fresh water, sediments and nutrients to estuaries has decreased in recent years, following exceedingly warm and dry conditions. South Australian estuaries are also likely to be negatively affected by pollutant inputs from development and alterations to inflow (Gorman et al. 2009, Dittmann et al. 2015). A similar scenario has unfolded in Western Australia, where hot, dry conditions reduced freshwater inflow and caused some estuaries to display persistent high-salinity conditions.

Historically, the Peel–Harvey Estuary in south-west Western Australia suffered from eutrophication, until the opening of the Dawesville Channel in 1994 increased tidal exchange, and resulted in higher abundance of seagrass, macrophytes and associated fish. These changes have been exacerbated in recent years, as the hot, dry climate has reduced freshwater inflow and created persistent high-salinity conditions, shifting the ecosystem even further towards a marine state (Potter et al. 2016). Although these changes can be viewed as positive from the standpoint of biodiversity, the opening of the channel failed to address the source problem of catchment inputs (Elliott et al. 2016). Reducing inputs at the source could be achieved by improvements in stormwater and agricultural run-off, assistance to landowners to manage inflow, and assignment of priority levels to address urgent hazards.

The environmental impacts of upstream development (e.g. dams and irrigation) on estuaries require greater consideration, particularly in northern Australia (see Water abstraction). Australian Government studies of predicted impacts of northern development have focused on rivers rather than estuaries, despite a history of comparable impacts on estuaries elsewhere in Australia. A recent study estimated that an investment of $350 million into the repair of Australian estuaries would be returned within 5 years from the subsequent increase in commercial fishing productivity and profit (Creighton et al. 2015).


Bays are moderately sized inlets on the coast, and are typically bedrock lined with high marine influence. Bays have historically been highly productive and diverse locations that supported Indigenous communities, as well as the economic activity and survival of early European settlements. Today, they still offer substantial economic value and lifestyle amenities. With some exceptions, management has largely failed to stem the loss and degradation of these habitats because of insufficient control of the primary drivers of change.

Most bays in New South Wales are exposed to limited catchment input, and many are ocean dominated (e.g. Byron Bay) and effectively open coast in terms of water quality. Although these bays are only exposed to limited contaminants from small nearby estuaries or the ocean, many are a focus for human activity and development (e.g. Coogee Bay, Bate Bar [Cronulla], Long Bay) and are hence exposed to urban run-off and pollution. No bays in New South Wales are pristine, but those on the south coast surrounded by national park (e.g. Bittangabee Bay) are less modified. Even these bays experience some human influence, however, including commercial and recreational harvesting of lobster, abalone, fish and other marine organisms. Exposure to contamination is likely to be relatively low for these bays except for widely dispersed contaminants (including litter) and shipping-related and boating-related contaminants.

Several of the largest embayments in New South Wales are the focus of large population centres and industry, usually because of their provision of safe harbours (e.g. Botany Bay). These have:

  • substantial contamination issues
  • high numbers of introduced species
  • elevated physical disturbance (e.g. frequent boat wake)
  • been subject to land reclamation
  • many artificial structures (e.g. piers, wharves).

However, like modified estuaries, many of these embayments support diverse and abundant marine life (Clark et al. 2015). Victoria has a similar pattern to New South Wales in embayment state, distribution and pressures. Water quality improvements have been made for Port Phillip Bay; however, the bay is subject to pressure from recreational and commercial fishing, the ongoing urbanisation of catchments, the introduction of invasive pests (e.g. sea stars and fan worms) and development proposals that are evaluated individually rather than within the context of cumulative stressors.

A lower proportion of bays in Queensland are degraded, since the high-population and industrial areas are positioned further inland and away from the embayments (e.g. Moreton Bay). However, some bays are affected by eutrophication and sediment input, however, which is reflected in the decline of their seagrass, and fishing has also modified the ecosystem of Moreton Bay. Most bays in Western Australia are considered pristine or very good, and none are heavily modified (in contrast to some Western Australian estuaries). In the Northern Territory, effects of human modification are predominantly restricted to Darwin Harbour. The large bays or gulfs of South Australia have lost 1500 kilometres of oyster reef throughout their range, and urbanised coasts have experienced some of Australia’s most extensive and intensive losses of seagrass beds and kelp forests.

The value of bays to society creates impetus for their protection, and some bays have been focal points for conservation via marine parks (e.g. Jurien Bay, Jervis Bay, Moreton Bay). Furthermore, a series of catchment and urban input strategies and management approaches have been developed to reduce pressures. These include initiatives by Landcare, catchment management authorities, and state and national environment and primary industry agencies, for progress in areas such as stormwater management and public education. Whether management can reverse the decline is an ongoing debate, as attempts are made with variable success.

Pressure from increasing populations and associated development means that the most likely outlook is for slow deterioration of bays as a habitat for species, despite mitigation and restoration efforts. Short-term change is, however, likely to be small, given that large changes have already taken place (e.g. Connell et al. 2008, Alleway & Connell 2015). In the longer term, effects of ocean warming and acidification will exert greater pressure, particularly in combination with existing local stressors. A recent global quantitative analysis suggests that bays may be disproportionately sensitive to future climate change (Nagelkerken & Connell 2015). Although direct and top-down effects of climate have attracted considerable attention and we are learning their effects (e.g. Karelitz et al. 2016), the bottom-up effects are barely recognised—yet potentially powerful (Connell et al. 2013).

Water quality (turbidity, physicochemical properties)

Water quality refers to the physiochemical properties of water, including salinity, temperature, turbidity, oxygen saturation and dissolved organic matter. Water quality is highly variable through space and time, and is often indicative of recent pressures. Processes that alter coastal water quality include catchment modification, agriculture, urbanisation, erosion, dredging and sediment resuspension.

Water quality is in good condition in many coastal areas, but is in worse condition near or downstream of population, industrial or agricultural centres. Although diffuse pollution from urbanisation and agriculture is the major driver of poor water quality, the expansion of major ports is often a higher-profile trigger for public concern. For example, in Queensland, a $20 million compensation claim was lodged by fishers and business owners in response to continued dredging (McCosker 2012).

Photosynthetic organisms such as benthic microalgae, seagrasses and macroalgae are directly affected by changes in the optical properties of water (i.e. turbidity, transparency and colour). Optical conditions are highly variable in space and time, but are affected by suspended sediments, tannins and phytoplankton. Heavily dredged and developed areas typically have poor water transparency.

Only a small proportion of the Australian coast has been field sampled for water turbidity, transparency and colour. Water quality information is typically collected at small spatiotemporal scales, or is collected as part of large disturbance monitoring programs, such as for dredging operations (however, see Box COA7 ). Ocean colour imaging is broadscale, but requires substantial field calibration. The Great Barrier Reef has received significant attention, where a large body of work describes the effects of increased sediment from rivers on lagoonal turbidity (e.g. Fabricius et al. 2014, 2016).

The outlook for water turbidity, transparency and colour in the short and medium term is good. Management is increasingly recognising the importance of water quality when considering future projects, and is implementing catchment stabilisation initiatives. In some areas, management actions have already led to improvements in water quality. In the longer term, climate change, particularly the alteration of precipitation and drought patterns, is expected to negatively affect coastal water quality.

Box COA7 National assessment of estuarine water quality using satellite data

Large-scale assessment of water quality change using traditional measurements is expensive. Modern methods such as remote sensing (analysis of data collected by satellites) have great potential for scaling up monitoring in powerful and efficient ways.

The analysis presented here uses colour measured by satellites as a proxy for water quality change. It is based on the idea that water with reduced quality tends to have an increased reflectance of red wavelengths. The aim was to study net trends of change (positive change, no change or negative change) in water colour in every Australian estuary, from 1987 to 2015.

Light reflectances of water in each estuary were obtained from the Data Cube, which is a collection of Landsat images processed and curated by Geoscience Australia and CSIRO. Spatial resolution is limited to areas of 30 metres × 30 metres, and days with cloud covering more than 50 per cent of the estuary were discarded. Land areas, very shallow waters and very coastal waters were masked out, and pixels were filtered using near-infrared reflectance. In addition, modelling was done using mean values per estuary per day. The effects of temporal periodicity and weather (rain) were first accounted for, and therefore the net trends observed in the results are caused by other factors, including human impacts.

Change in the ratios of reflectance of green light versus red light and blue light versus red light were used to estimate change in water colour. Increases in the ratio indicate positive change in water quality, whereas decreases indicate negative change. The results showed that most estuaries have the same trend for both the green–red and blue–red light ratios, although some differ (Figure COA12).

Model predictions were validated by correlating trends in time as shown by the model with trends in data collected by traditional turbidity measurement methodology, such as Secchi disks, turbidity sensors and total suspended solids, for 22 Australian estuaries. This validation method shows that the temporal trends of the ratios are positively correlated with those obtained for increasing Secchi depth (increased water clarity), and mostly negative correlated with increasing turbidity, total suspended solids and chlorophyll. These results indicate that reflectance ratios may be a useful proxy for water quality conditions.

Source: Bugnot AB, Lyons M, Clark G, Fyfe S, Griffin K, Lewis A, Scanes P, Johnston E (collaboration between the University of New South Wales [NSW], the NSW Office of Environment and Heritage, and Geoscience Australia).

Clark GF, Johnston EL (2016). Coasts: Coastal waterways. In: Australia state of the environment 2016, Australian Government Department of the Environment and Energy, Canberra,, DOI 10.4226/94/58b659bdc758b