River health assessments in
Wilson Inlet catchment

Our rivers and streams are highly valued for the wide variety of social, cultural, recreational, environmental, and economic services they provide. These include water sports, fishing and marroning, nature-based recreation and ecotourism, and water supply for a range of agricultural, industrial, and urban uses. 

A properly functioning ecosystem supporting native biodiversity is critical to maintaining the intrinsic values of rivers and the essential services they provide. However, because of our use of rivers and the development pressures they face, aquatic ecosystems are exposed to significant and increasing stress.  Notable impacts include changes to natural flow patterns and connectivity (interrupting species migrations and flushing), poor water quality, reduced instream and fringing vegetation and habitat, and introduction of exotic species (which predate and/or compete with native species and bring disease and parasites).

The more stress our environmental systems face, the less they are able to tolerate and adapt to a changing climate, pressures from expanding and intensifying development, and increased frequency and magnitude of bushfires.    

Summary of river health

The major rivers in the Wilson Inlet Healthy Estuaries WA catchment are the Denmark River and Hay River. A total of 13 river health sites have been assessed in the catchment since 2009 under the department’s Healthy Rivers program. This includes targeted assessments in 2020 during the Regional Estuaries Initiative to investigate key areas of the catchment that previously had little or no data. Information from these assessments was examined  to assess the status of values and threats.

This work, and previous surveys, established that the biodiversity of waterways of the Wilson Inlet catchment is remarkably high, with 20 native fish and freshwater crustacean (crayfish and shrimp) species recorded within the catchment. Fifteen of these species are endemic to the South West of Western Australia (WA), which means that they are not naturally found anywhere else. This represents one of the highest biodiversity river systems across the South West.

The Department of Water and Environmental Regulation’s (the department) standard methods for assessing river health include collecting comprehensive data on water quality, fringing vegetation, flow, land use, and aquatic habitat, as well as the aquatic biodiversity, as described in more detail below. The biodiversity status is established by comparing the observed native and exotic species to those expected for each subcatchment, where the expectations are based on historical records. The 2020 assessments in the Denmark River catchment found most of the expected fish and crustacean species, and a high richness of macroinvertebrates (54 taxa across 34 families).

However, ongoing pressures and stressors to the aquatic ecosystems were identified, including:

  • excess nutrients
  • elevated salinity
  • clearing of native vegetation and associated impacts to streamflow, aquatic habitat and water quality (with ecosystem sensitivity to land use change increasing due to a drying climate and reduced rainfall)
  • exotic species - although only one exotic species has been recorded, the eastern gambusia, it is highly invasive and competes with native fish species
  • increased pressure on water resources with predicted expansion for agriculture and plantations.

The recent assessments were not an exhaustive survey of the current status of the entire catchment, however, the new data now adds to our knowledge base of how WA river systems function in different circumstances. The data also provides a baseline for ongoing monitoring of the health of the rivers in the catchment.

River health assessments

The Healthy Rivers Program carries out assessments of river health across the South West of Western Australia. This monitoring helps to determine and prioritise management actions, based on values, threats and stressors identified. The assessments also establish a benchmark from which the success of management activities can be determined into the future.  The river health assessments carried out in November 2009 were part of a broader program of sampling method development and application to sites across the South West of WA. Results are summarised here.

Four new sites were assessed in March 2020, through the Healthy Rivers program under the Regional Estuaries Initiative. The sites were:

Additional surveys of aquatic fauna were also conducted at the following sites (as full river health assessments were not carried out, these sites have not been included in the total number of sites assessed in the Wilson Inlet catchment):

  • Muir Highway 1 (Hay River)
  • Muir Highway 2 (Hay River)
  • Mitchell River bridge (Mitchell River – tributary of the Hay River)

Aquatic biota

Based on recent assessments and available historical data, the Wilson Inlet catchment is home to 20 species of native fish and freshwater crustaceans (crayfish and shrimp). This includes 12 freshwater fish (five of which have conservational significance), two freshwater-estuarine species, five freshwater crayfish and the freshwater south-west glass shrimp.  One exotic fish has also been observed.  Fifteen of these species are endemic to the South West of WA, which means that these species are not naturally found anywhere else.

The crayfish fauna includes a new species, which was discovered through a recent genetic survey of crayfish species in the south-west. The species appears to be confined to the Denmark-Albany region and is similar in appearance to the restricted gilgie (Cherax crassimanus). This species of crayfish is yet to be described, for the purpose of this summary it will herein be referred to as C. species novel. This further highlights the unique biodiversity of this area.

Only one exotic species was recorded in the Denmark and Hay River systems, the eastern gambusia. The presence of only one exotic species likely demonstrates that the systems are in a relatively natural condition. Exotic species tend to have greater tolerances for the more extreme conditions (low dissolved oxygen and elevated water temperatures) and as such often dominate native fish when the ecosystem is under stress. Such conditions are more likely to occur where natural conditions have been disturbed, for example where land clearing occurs with follow-on impacts such as erosion and sedimentation, increased nutrient run-off, and a loss of habitat for native aquatic and semi-aquatic species.

Species that have previously been observed in the estuarine section of the catchment (not included in the table below) include estuarine cobbler, tarwhine, Australian herring and yelloweye mullet.

Other non-targeted native species recorded in the catchment include bush rat, native water rat (rakali) and south-western snake necked turtle.

Native species (Click for more information)

Green border indicates species with conservational significance

Non-native species:
Other non-targeted native species:
From all historical data including the 2020 data, species richness (the number of species found) has been determined for the different parts (subcatchments) of the Wilson Inlet catchment; up to 12 different fish and crayfish have been found in some areas (left map below). Notably the highest richness of native species occurred in the forested catchments (see land use section). The map on the right shows subcatchments where the exotic species has been found.
These maps are based on the data reported to DPIRD as a requirement of species collection licenses. Data used in the map covers up to 2017 for non-DWER projects, and up to 2020 for DWER projects.

The river health assessments on the Denmark River in March 2020 were focussed around the public water supply dams on the lower section of the catchment. Additional traps were placed at locations on the Hay River to opportunistically fill gaps in knowledge of species distribution (a full river health assessment was not completed at these sites).

The sites assessed on the Denmark River recorded a total of ten native species, including five native fish (western pygmy perch, western minnow, common jollytail, blue-spot goby, nightfish) and four native crayfish (gilgie, Cherax species novel, koonac, smooth marron) and freshwater shrimp. One exotic fish species (gambusia) was found.

Of note, some of the largest western minnow and nightfish found across all assessments conducted under the Healthy Rivers program (over 800 site assessments between Jurien Bay and Esperance since 2008) were recorded in the densely forested section of the catchment on the Quickup River. The furthest upstream assessment site on the Denmark River recorded four native crayfish (gilgie, Cherax species novel, koonac, smooth marron). This diversity of crayfish species at one site, where typically one or two are observed, highlights that the Denmark River supports a range of niche habitats for each species. Other non-targeted species observed include the south-western snake-necked turtle, native bush rat, and motorbike frog.

The five species of conservation significance that have previously been found in the catchment (mud minnow, Balston’s pygmy perch, little pygmy perch, black stripe minnow and lamprey) were not found in the 2020 sampling. The absence of three of them, Balston’s pygmy perch, little pygmy perch and the black stripe minnow, is not concerning as the subcatchments where they have previously been found were not sampled in 2020. Namely, based on previous data the distribution of both the Balston’s pygmy perch and little pygmy perch is further upstream in the catchment, and the black stripe minnow has only been recorded once in 2013 on the Hay River.

The mud minnow was expected but not found at the Quickup River site. This rare species was last recorded in 1995 and is highly susceptible to salinisation. Salinity at the Quickup River site was slightly elevated (1,200 mg/L, categorised as marginal-brackish), which may have impacted this species range.

Pouched lamprey are rarely caught in traps given a very short migration period as adults, and as ammocoetes (larvae/juveniles) largely remain buried in sediment in localised habitats, as such their absence in traps is not considered to reflect their absence in the system.

Macroinvertebrates were collected in March 2020 at three sites situated on the Denmark River. Macroinvertebrates play a vital role in stream ecosystem function and are valuable indicators of stream health. A total of 54 taxa (34 families) were collected across the three sites. Taxonomic richness increased with distance downstream. All three sites had macroinvertebrate communities which suggested some level of anthropogenic impact (human impact on the environment) such as nutrient enrichment, low dissolved oxygen, and salinisation. However, several more sensitive taxa were also recorded, which suggests that there are good water quality and habitat conditions present on the Denmark River, largely a result of the intact instream habitat and riparian vegetation.

Additional fauna assessment sites were conducted at two locations on the Hay River and one location on the Mitchell River (tributary of the Hay River). These were opportunistic surveys in easily accessible areas, as opposed to targeting key refuge areas (as is done for most assessments) and may not represent the aquatic fauna of the area.

A total of five native species (and no exotic species) were recorded on the Hay River system, including two freshwater fish (western minnow, nightfish) and three freshwater crayfish (gilgie, koonac, Cherax sp. novel).

The site on the Mitchell River (Mitchell River Bridge) was a series of small and shallow pools. Koonac, Cherax species novel, nightfish and western minnow were found. Importantly, juveniles of the latter three species were abundant, indicating that this site serves as an important nursery ground within the Mt Lindsey National Park.

The native water rat (Rakali) was also observed on a motion sensor camera at a site on the Hay River (Muir Highway 2). It is significant to have observed this species as numbers have been declining, due to loss and degradation of streamside habitat, salinisation of waterways (also impacting food sources), and predation by introduced species such as cats and foxes.

Hydrology and landuse

The two major rivers in the Wilson Inlet catchment are the Denmark and Hay Rivers, which extend 50 km and 80 km inland, respectively.

Approximately 47% of the catchment is cleared of native vegetation, with the cleared areas predominantly occupied by livestock for grazing (cattle and sheep), plantations, and cropping. Large areas throughout the middle of the basin have been set aside for conservation (Mount Lindsey and Mount Roe national parks) and managed resources (state forest).

 There have been considerable modifications to the drainage of the catchment from its natural state. Two dams have been built for potable water in the Denmark River system, one on the main channel and another on the Quickup River tributary. There are also many private farm dams throughout the catchment. Artificial drainage is present throughout agricultural areas of the catchment. Portions of Cuppup Creek and Sleeman River have been artificially modified to improve localised drainage.

Modifications to drainage and damming of rivers may have a large impact on aquatic ecosystems. It not only alters the natural flow regimes (i.e. the magnitude, frequency, duration, timing, and rate of change of flow events), it also largely effects the evolved life history stages of associated flora and fauna. Impacted aspects may include fish movements (life stage triggers, foraging, breeding, habitat), innundation of riparian vegetation, erosion and sedimentation, longitudinal and lateral habitat connectivity and water quality.

Mean annual rainfall in the region varies from 1050 mm in coastal areas to 650 mm around the headwaters. However, rainfall in Denmark has been steadily declining since the 1970s. Since 2010, Denmark has received record low rainfall on five separate years (in 2010, 2013-14, 2018-19).

Reduced rainfall has contributed to significant drops in streamflow in the catchment. On the Denmark River this is most obvious in the middle to upper sections, where the river has seen longer and more frequent periods of no flow over summer since 2010.

The Hay River generally flows throughout the year, occasionally ceasing to flow over summer in recent years (since 2008).

In the 1980s and 1990s, the Denmark River was showing signs of salinisation (increasing salt levels), as has occurred in many other Australian rivers. The increase in salinity was due to clearing of native vegetation for agriculture; the resultant rising groundwater levels carried salts from the soils into waterways. Due to a range of management interventions in the upper catchment, Denmark River is the only river in Australia to show signs of from rising salinity. However, continued monitoring of streamflow, salinity and groundwater levels is required to support continued management of the aquatic ecosystem and water resource, particularly considering the drying climate trend. Maintenance of forest cover is essential to ensuring stream salinity remains low.

Vegetation, physical form and habitat

The fringing vegetation of the Denmark River is largely intact and in good condition. The upper and middle sections of the catchment are mostly forested. The lower catchment is vegetated along the riverbank but becomes increasingly cleared adjacent to the fringing vegetation along the river towards the inlet. The fringing vegetation along the Hay River is in poor condition in the top half of the catchment and is mostly cleared for agriculture (including plantations) adjacent to the river. Vegetation condition generally improves moving downstream and in catchments of tributaries to the west/south-west, where intact forest remains.

At the assessment sites on the Denmark River, fringing vegetation was in good condition with all structural layers intact (lower, middle and upper storey). The width of vegetation along the river was variable, ranging from dense forest to a narrower strip (15 m) of remnant vegetation beyond which it was cleared for agriculture (see Hydrology and land use ).

Evidence of bank erosion was not obvious at any of the sites. In-stream habitat at the assessment sites was found to be in good condition, with stable banks, good stream shading, vegetation draped in water along most of the bank, an abundance of woody debris in a range of sizes, and detritus covering the riverbed.

Water quality

Longer-term water quality monitoring has been carried out by the department at several sites in the Denmark Catchment (see map above). The monitoring includes a site, downstream of the Riverbend Lane river health assessment site, on the Denmark River. Seasonal and longer-term trends in nutrients, salinity, total suspended solids, and pH are monitored. The longer-term monitoring (2004-18) shows the Denmark River has fresh to marginal salinity (less than 1,000 mg/L). In contrast, the has ranged from brackish to saline (up to 7,000 mg/L) with an increasing trend over the 2012-18 period.

Nutrient concentrations (total nitrogen and total phosphorus) in the Denmark and Hay rivers remained below guideline levels (ANZECC trigger values for lowland rivers in South West WA) from 2004-18 (1.2 mg/L and 0.065 mg/L, ). Elevated concentrations have been recorded on some occasions in the Hay River, because of agriculture and cleared native vegetation in the catchment.

Water quality samples from previous river health assessments (November 2009) were consistent with the longer-term monitoring, indicated good water quality with exception of the assessment site in the upper catchment on the Hay River. This site had the highest total nitrogen of the sampled sites (equal to the guideline value, 1.2 mg/L) and the water was saline.

Four river health assessments were carried out in March 2020, peak dry season (February to March). This targetted the time of year when the ecosystem is under most stress due to lower water levels, reduced flow and higher temperature. Higher temperature and salinity, combined with lack of flow, may contribute to lower dissolved oxygen concentrations.

Salinity at all four assessment sites was in the marginal category (salinity 500-1000 mg/L), with higher salinity at the Quickup River site than the three Denmark River sites. Water quality was generally within acceptable levels for pH, temperature and nutrients. However, dissolved oxygen concentrations were below 4 mg/L at the three sites on the Denmark River (ranging from 1-4 mg/L). These concentrations are below tolerance levels of most aquatic fauna (Beatty et al., 2013), with increasing levels of stress expected below 4 mg/L, and mortality typically seen below 2 mg/L. The continued high biodiversity suggests that higher oxygen refuge habitats exist elsewhere in the system. Further deterioration of oxygen availability is likely to have significant impacts, especially if persistent low oxygen conditions occur throughout the water column. It should be noted that the effect of low oxygen on communities typically follows a threshold-response, where an acute impact to all species is seen when conditions reach at specific point, rather than a slow decline in health and/or abundance.

In contrast to the low dissolved oxygen at the assessment sites on the Denmark River, the dissolved oxygen concentration at the Quickup River site (a tributary of the Denmark River) was above the recommended guideline, with concentrations of 5-6 mg/L.

Beatty, S, Morgan, D, Keleher, J, Lymbery, A, Close, P, Speldewinde, P, Storer, T & Kitsios, A 2013, Adapting to climate change: A risk assessment and decision making framework for managing groundwater dependent ecosystems with declining water levels. Supporting document 4: Environmental variables in the habitats of southwestern Australian freshwater fishes: An approach for setting threshold indicator value, National Climate Change Adaptation Research Facility, Gold Coast, 33 pp.