6. Factors influencing the Region’s values

It has been long recognised that, due to changes in land use following European settlement, the Region’s values are threatened by poor water quality resulting from increased concentrations of suspended sediment, nutrients, pesticides and other pollutants (Section 6.5.1).⁴² The risk of specific pollutants — including the severity and duration of exposure, and the species, habitats and ecological processes affected — varies across the Region.¹⁸⁸⁰ Risk from pollutants is influenced by the volume and timing of seasonal rainfall and subsequent runoff events, which are determined by the highly variable monsoonal climate (Box 6.1) and extreme weather events, such as cyclones and hydrodynamic factors, including tidal regimes and currents.⁶⁹³ 

Pollutants in land-based runoff can affect ecosystem resilience by reducing biodiversity and destabilising ecosystem functions and services.^1840,1881 Inshore areas of the Reef experience the greatest impacts, whereas mid-shelf and outer reefs are less frequently affected due to their distance from river mouths and the primarily northward dispersion of most river plumes.⁵²⁸ However, after large rainfall events and under atypical hydrodynamic conditions, flood plumes can reach these more distant areas,^586,919,1882  as evidenced by the Burdekin River floods in 2019.⁷⁷¹ 

Understanding the exposure of the Region’s ecosystems to pollutants in land-based runoff is important for identifying the most vulnerable areas and setting specific targets for reduction of pollutants entering the coastal and inshore areas ¹⁸⁸³ (Section 6.5.1). Areas adjacent to the Wet Tropics, Burdekin and Mackay Whitsunday regions are of particular concern given their high loads of dissolved inorganic nutrients, suspended sediments and pesticides, respectively.⁶⁹³ Inshore ecosystems such as seagrass meadows and coral reefs are the most susceptible to impacts due to their proximity to pollution sources. Different pollutants can combine to produce compounding effects. For example, both elevated levels of suspended sediment in the water column, and the proliferation of phytoplankton caused by increased dissolved nutrients, reduce the available light for benthic organisms, such as corals and seagrasses.^175,1840

Inshore ecosystems generally exhibit a capacity for recovery in the absence of acute events, such as cyclones and large river discharge,^175,573 though this capacity can be reduced by chronic exposure to other stressors.^1880,1884 For example, in 2019 the Burdekin floods caused significant decline in seagrass condition, but by 2022 in the absence of major weather events, the condition of seagrass had started to recover, likely driven by the presence of large seed banks.¹⁴⁵ Chronic impacts of poor water quality caused by land-based runoff can lower the resilience of ecosystems making them vulnerable to future disturbances.^573,1405 The frequency of exposure to river plumes is negatively associated with the ability of corals ^573,1405 and seagrasses ⁵⁷⁶ to recover after disturbance.

Nutrients

Excess nutrients from land-based runoff can cause significant deleterious impacts on the Reef’s ecosystems. Nutrients are chemical elements or compounds that are essential to life but, when present in excessive amounts, can cause negative ecological consequences.^132,571,1840 Most discharge of nutrients from rivers to the Region occurs in the summer wet season, from December to April. Microbial mineralisation and mobilisation of particulate and organic forms are also important sources of bioavailable nutrients.⁵⁹⁵ 

Excess nutrients are associated with increased biomass of phytoplankton and zooplankton primarily in the inshore area.⁷⁰³ Phytoplankton biomass responds positively to nutrient availability, leading to phytoplankton blooms following discharge of nutrient-rich flood waters.¹⁸⁸⁵ The impact of elevated phytoplankton on coral reefs and seagrass meadows is mostly via reduction of water clarity and consequently light availability for the photosynthesis of corals and seagrasses.^132,276

Elevated nutrient levels, particularly dissolved inorganic nitrogen, have been associated with a lowering of thermal bleaching threshold in corals in the Region.^276,733,1886 Nutrients can also affect the coral microbiome, resulting in microbial imbalance (dysbiosis) and coral disease. Although nutrient enrichment can be broadly associated with coral disease, relationships with specific nutrient forms remains unclear.⁷³¹ On inshore reefs, the influx of land-based nutrients is associated with high cover of macroalgae. Once established, macroalgae are often highly persistent, as density-dependent feedback loops reinforce their competitive advantage relative to that of corals.¹⁸⁵ As a result, high macroalgal cover often hinders the recovery of coral communities after acute disturbances, such as heat stress or cyclones.

Seagrasses can also be indirectly affected by nutrients. While elevated nutrients can enhance seagrass growth,¹⁸⁸⁷ they also promote the growth of phytoplankton, macroalgae, and epiphytic algae, which results in reduced light attenuation for seagrass leaves.¹⁸¹⁸ Epiphytes and macroalgae can compete with and block light reaching seagrass leaves, thereby compounding environmental stress.¹⁴⁵ In the inshore seagrass monitoring sites, decreasing and low epiphyte cover on seagrass leaves across coastal habitats, accompanied by continued low macroalgae abundance across all habitats, has contributed to the recovery of seagrass meadows in the Region.¹⁴⁵

Nutrient enrichment has also been often cited as a factor driving outbreaks of crown-of-thorns starfish ¹⁰¹⁰ (Section 3.6.2). Nutrients from land-based runoff during heavy river discharge events, which sometimes coincide with the pelagic phase of developing larvae, can result in phytoplankton blooms that increase the amount of food available for crown-of-thorns starfish larvae.⁷³⁵ The observed sensitivity of crown-of-thorns starfish larvae to low-salinity waters associated with flood plumes ⁷⁶⁸ may partially explain why crown-of-thorns starfish are less common on inshore reefs. However, this sensitivity does not preclude a role for increased planktonic productivity linked to land-based runoff having positive impacts on larval survival and development.¹⁰²¹ Although the role of nutrient enrichment in crown-of-thorns starfish outbreak dynamics remains unresolved,^735,1888 recent findings suggest only a weak link between the influx of nutrients from land-based runoff and the modelled response of phytoplankton productivity in the primary initiation zone of crown-of-thorns starfish outbreaks in mid-shelf waters of the Wet Tropics.⁷³⁸ Oceanographic processes, such as upwelling and intrusive events, may be more important drivers of inter-annual variability in nutrient concentrations in this area than previously understood.^735,738

Sediments

Influx of fine sediments from large flood events can have long-lasting impacts in ecosystems. Immediately after flood events, and for a few months afterwards, fine sediments can stay resuspended in the water column and decrease availability of light reaching the seafloor.³⁹ Flood plume sediment is often associated with increased nutrients delivered to inshore areas, which can favour an increase in macroalgal cover, affecting both coral and seagrass communities.^145,185 Sediments deposited on the seafloor can also increase turbidity through chronic wind- and current-driven resuspension, reducing photic depth for long periods of time.^1889,1890 Fine sediment primarily affects shallow inshore coral and seagrass communities, and organisms that rely on them.^{185,145,1891,576} In reef fish, excess sediments can affect some species by inducing changes in feeding behaviour due to increased sediment loads within algal turfs, ^1892,1893 doubling larvae development time,¹⁸⁹⁴ reducing growth rates,¹⁸⁹⁵ reducing the ability to find suitable habitat,¹⁸⁹⁶ changing predator–prey interactions ¹⁸⁹⁷ and damaging gill structure.¹⁸⁹⁸

Corals are highly sensitive to chronic exposure to fine sediments, which affects their biology by reducing recruitment and settlement success and smothering adult colonies.^{39,910,1899,1900} At community level, in the Mackay Whitsunday region, coral communities have been slowly recovering from legacy effects of cyclone Debbie, which severely affected the region in 2017.¹⁹⁰¹ Following the severe loss of coral cover at many sites post-Debbie, successful recovery relied heavily on the recruitment and survival of juvenile corals, which were significantly reduced by fine sediments present in the water column and deposited in shallow areas. Over the past 5 years, fine sediment deposited by cyclone Debbie has naturally and gradually moved away from the inshore reef region, allowing space for new corals to settle. Even though the density of juvenile corals continued to increase in past 2 years, juvenile density remains low on most reefs, suggesting a bottleneck for the recovery of these communities. Included among the increasing numbers of juveniles are the fast-growing genus Acropora; the survival and growth of these colonies will be central to the recovery trajectory of the coral communities in coming years.¹⁸⁵

Fine sediments can affect seagrass condition by smothering plants and limiting light.¹⁸⁹⁰ The respiratory requirements for survival and growth cannot be met by photosynthesis under low light conditions.¹⁹⁰² In inshore sites, seagrasses are often exposed to a very high frequency of turbid water resulting from resuspended fine sediment, even in low-discharge years. These turbid waters constrain the depth limit of seagrass occurrence and, therefore, influence their spatial extent and cause changes in abundance and resilience.¹⁴⁵ In extreme cases, when the disturbance is long-lasting, plant death, changes in species composition or even meadow loss can be observed. ¹⁴⁵ The loss of seagrass meadows can have an indirect impact on dugong populations, as dugongs are highly dependent on seagrass for their diet.^1903,1904 Reduction in dugong populations, either by migration or by death from starvation, has been linked to reduced seagrass abundance in some areas of the Reef.^520,1904

Pesticides

Pesticides are found ubiquitously in the Catchment and inshore areas of the Region.^{1905, 1852,1830} Concentrations of pesticides above Australian guidelines are often found adjacent to and downstream of areas of horticulture and intensive cropping, particularly sugarcane.¹⁸⁴⁷ These areas are largely located in the Wet Tropics, Burdekin and Mackay Whitsunday regions. 

Mean contributions of individual pesticides in catchment waterways and inshore areas also vary between regions. Pesticide risk and toxicity are assessed collectively as opposed to individually for each pesticide.¹⁸⁵⁰ In inshore areas of the Mackay Whitsunday and Wet Topics regions, diuron, imidacloprid and hexazinone are common, whereas tebuthiuron is often detected in the Burdekin inshore region.^1855,1830 ‘Alternative’ photosystem II and non-photosystem II herbicides are increasingly applied as substitutes for effective weed control to help achieve targeted reductions in priority herbicide loads.¹⁹⁰⁶ However, alternative herbicides can exhibit similarities in physico-chemical properties to the priority photosystem II herbicides and, in some cases, can be just as toxic to non-target marine species.¹⁹⁰⁷ Links between organism responses and pesticide exposure in the field are uncertain due to the possibility that other environmental factors, such as temperature, light and other pollutants, can confound responses.¹⁸⁴⁹ In addition, mixtures of pesticides can be associated with higher or lower risk than individual pesticides, depending on the specifics of chemical interactions.¹⁸⁵²

In the environment, pesticide runoff losses and degradation vary significantly among different types of pesticides. For example, PSII herbicides, such as diuron and atrazine, which are commonly found in the environment, are estimated to have half-lives between 40 and 100 days, respectively.^1846,1908 Although persistence in the environment is lower than some legacy pesticides (such as organochlorine pesticides like DDT), PSII herbicides can persist in marine waters for a significant period of time.¹⁹⁰⁹

While in situ impacts of pesticides are difficult to quantify, deleterious effects have been studied in Reef organisms under controlled laboratory conditions. Pesticide toxic effects have been extensively demonstrated on organisms that rely on photosynthesis for growth and reproduction, such as seagrasses, hard corals, crustose coralline algae and symbiont-bearing foraminifera.^{1910,1911,1912,1913} Among pesticides, PSII herbicides are commonly studied due to their extensive use and ubiquitous presence in the marine environment.^1855,1830 Diuron has been shown to impair photosynthesis and reduce calcification rates in corals and in the calcifying algae Halimeda under short-term exposure.^1907,1914 Photosystem II herbicides also negatively affect the growth and photosynthetic efficiency of coral symbionts.¹⁹¹⁵ Growth rates of and photosynthesis in marine microalgae are also affected by herbicides.^1907,1916

In addition to herbicides, exposure to several insecticides (diazinon, fipronil and imidacloprid) and fungicides (chlorothalonil and propiconazole) has been shown to negatively affect all life-history stages of corals.¹⁹¹⁷ Insecticides inhibit fertilisation and metamorphosis, as well as reduce coral settlement.^1917,1918

Pesticide concentrations in the inshore Reef are typically highest over the summer wet season,¹⁸⁵⁶ making inshore areas frequently co-exposed to herbicides and high seasonal water temperatures, which exacerbates the toxic effects of pesticides in reef species.^{1914,1919,1920} However, the cumulative effects of heat stress and pesticides on ecosystems remain poorly understood. 

Marine debris

Marine debris is a major threat to the health and values of the Region and causes mortality of marine turtles, dugongs, dolphins and seabirds.^1865,1921 Marine debris is commonly found in the Region; however, the sources of marine debris, particularly plastics, vary with geographical position. Land-based sources contribute approximately 80 per cent of anthropogenic debris in marine environments. The vast majority of debris found in the Region is plastic.¹⁹²² Land-based runoff and stormwater systems are believed to be the main source of marine debris and plastic in coastal and inshore areas.^1923,1872 Islands are often the repository of windborne plastics, as well as general waste associated with tourism activities (fishing, boating and presence on islands), commercial boating and fishing, and localised stormwater runoff.^{1867,1868,1869,1924} Marine debris can float, sink, become entangled on rocky outcrops or reefs, or become buried in the sea floor where it can resurface after disturbances, such as cyclones and floods.¹⁹²¹ It can also break down into smaller particles with long-lasting impacts in the environment.¹⁹²⁵ 

Marine microplastics can bioconcentrate and bioaccumulate in reef organisms, but in contrast to other pollutants such as metals, biomagnification is not as common as previously described.^{383,1480,1862} Microplastics also act as carriers for a range of toxic substances.¹⁹²⁵ Ingestion of microplastics is common and can affect the health of corals, fish, marine turtles, seabirds and cetaceans.^{1926,1927,1861,1862} Coral reefs, and reef-building corals, in particular, intercept and accumulate microplastics.¹⁹²⁸

Other pollutants 

In the Region, pollutant sources — such as agriculture and mining runoff, ports and harbours, drainage from acid sulfate soils, industrial effluents and emissions, atmospheric deposition, urban centres and wastewater discharge — all contribute to elevated concentrations of metals and metalloids in receiving waters.¹⁸⁶⁷ Metals are highly persistent and remain in the environment indefinitely, binding to fine particulate sediment and settling on the substrate where concentrations are absorbed by reef organisms. Often, metals bioaccumulate at greater concentrations than those detected in the surrounding environment.¹⁹²⁹ High metal concentrations have been detected in inshore seagrass meadows, which are a key food source for some species of marine turtles.^1930,1931 Turtles are also known to graze on turf algae. Elevated metal loads in seagrass and turf algae could translate into accumulation of metals in turtle tissues.¹⁹³² Similar accumulation could also occur in herbivorous and detritivorous reef fishes. High metal concentrations may also alter fish feeding behaviour.¹⁸⁷⁶ Accumulation of metals in key food sources for herbivorous animals may represent a pathway through which metals enter reef food chains and cause deleterious effects to marine mammals and other apex predators.

Many pharmaceuticals and personal care products, such as ultraviolet light filters and antibiotics, are persistent, bioaccumulative and potentially toxic.¹⁹³³ They may, therefore, affect the health of reef organisms. However, the persistence and potential impacts of such products on reef ecosystems are knowledge gaps.

Persistent organic pollutants (POPs) often bioaccumulate in food webs and can cause deleterious effects on growth, reproduction, metabolism and survival of reef organisms.¹⁸⁷⁹ These products often have long half-lives that range from decades to centuries. They are considered resistant to metabolic, chemical, microbial and photolytic degradation procedures.¹⁹³⁴ However, the toxicity of POPs, such as petroleum hydrocarbons, can substantially increase in the presence of ultraviolet light, causing severe impacts on the settlement of coral larvae in shallow reef environments.^1935,1936 Exposure to oil derivatives can also alter habitat settlement and antipredator behaviours, reduce sheltering and shoaling, and increase risk taking in reef fish. These effects all exacerbate predator-induced mortality during recruitment, resulting in disruption of early life-history stages.¹⁹³⁷