Healthy Estuaries WA is dedicated to protecting and improving the health of estuaries in the state’s south west, including Wilson Inlet. Scientific understanding is key to effective management. 

Since October 2016, the Department of Water and Environmental Regulation has monitored Wilson Inlet’s water quality at seven sites every two weeks. The first 12 months of data (October 2016 to September 2017) has been compiled to give a comprehensive overview of the annual condition of the estuary. 

In 2016/17 Wilson Inlet monitoring data show a healthy and productive estuary. However, it does show impacts of excess nutrients flowing in from the catchment at particular times of year. 

Wilson Inlet’s water quality is strongly influenced by the freshwater inflows from rivers and by the sandbar separating the inlet from the ocean. The bar is usually dredged in winter to stop low-lying lands flooding after winter rainfall. It naturally closes due to waves depositing sand to reform the bar in late summer or early autumn each year. In 2017 the bar was closed for 6 months, from 23 February to 24 August. 

2017 was an average rainfall year, however most of the rain fell in late winter and early spring and therefore the sandbar was opened in late winter.  

When the bar was closed the water was brackish, well-mixed, oxygenated from the surface to the bottom with low concentrations of nutrients and algae – all signs of healthy conditions. In contrast, when the bar was open, salinities ranged from fresh to marine, nutrient concentrations were higher due to the nutrient-rich inflows from the catchment and consequently there was more algal growth. 

When the bar was open, marine water entered the estuary and formed a heavier, salty layer underneath the brackish estuary water (stratification). When stratified, nutrients were released from sediments due to chemical changes caused by low oxygen conditions (hypoxia) in the bottom layer.  

Overall microalgae densities were low, however, three periods of higher algal densities were observed; two of them during the bar-open period in spring 2016 and 2017 and one in autumn 2017.  There were no reported fish kills or harmful algal blooms. 

For the current monitoring period there were no nuisance algal blooms in Wilson Inlet. There were four occasions throughout the monitoring period when levels of potentially harmful algae exceeded safe levels for shellfish consumption.  

Approximately 35 per cent of Wilson Inlet has a healthy seagrass habitat mainly consisting of the species Ruppia megacarpa. Ruppia plays an important role in absorbing nutrients from the water column and the sediment. With the current nutrient run-off into the estuary, if Ruppia was absent it would likely be replaced by less-desirable macroalgae or microalgal blooms. 

Despite some high nutrient inputs, the estuary is resilient for several reasons – the sediments have good phosphorus-binding capacity, the abundant seagrass (Ruppia) absorbs nutrients, and strong prevailing wind regularly mixes the water, breaking down the stratification. 

Nutrients entering the Inlet from the catchment and reduced winter flows due to climate change remain the highest risks to Wilson Inlet. Healthy Estuaries WA continues to support and focus on efforts that address nutrient inputs from agricultural and urban sources. 

Summary data 2016/17

Outline map of Wilson Inlet sites

This map shows how the 7 monitoring sites are grouped into 3 zones.

Sites are monitored fortnightly. The 2016/17 summary data for each estuary zone presents the annual means and standard deviations of 6 key water quality indicators – salinity, oxygen, water clarity, nitrogen, phosphorus and algae (microscopic).


There is a large variability in the salinity of Wilson Inlet depending on rain flowing in from the catchment and whether the bar is open or closed. When the bar was open, the salinity of Wilson Inlet varied between the surface and the bottom of the estuary, caused by the heavier marine water entering the estuary and creating a layer below the less dense brackish water (stratification).  When the bar was closed, without water exchange with the ocean and with strong prevailing winds, the waters were well mixed and salinities were consistently around 27 ppt.


Dissolved oxygen

Dissolved oxygen is the amount of oxygen dissolved in the water through absorption from the atmosphere and/or as a result of photosynthesis by seagrass or algae.

When the bar was open, most zones had healthy dissolved oxygen levels, the only exception was the central bottom waters which had episodes of very low oxygen levels due to the breakdown of organic material and a lack of mixing caused by stratification.

When the bar was closed, dissolved oxygen concentrations ranged from 8-9 mgL-1 in surface and bottom waters. These results indicate excellent water quality.


Water clarity

Water clarity is a measure of how far light penetrates into the water.

The water clarity was reasonably good when the bar was closed. There was less light penetration when the bar was open but still enough for healthy seagrass growth in depths to three metres.

*Water clarity is measured as Secchi depth



Nitrogen is are measured as nitrate and ammonium depending on their source however, both contribute to the overall nutrient levels in estuaries. Both of these forms are dissolved and readily available to algae for growth.

When the bar was open, nitrate-nitrogen levels were close to the guideline value in surface waters. Freshwater inflows are the main source of nitrate and high concentrations in the estuary represents a leakage of agricultural fertilisers from the catchment which fuels algal activity. When the bar was closed and less water was flowing in from the catchment, nitrate was well below the guideline values.

Ammonium-nitrogen was close to the guideline value for the most part. The bottom waters of central basin sites were well in excess of the guideline. This was most likely due to the release of ammonium, from the sediments during very low oxygen (anoxic) conditions caused by stratification.

The guideline values are an indication of the approximate nitrogen levels that may impact the health of an estuary.*Guideline is the ANZECC (2000) guideline value for south-west estuaries

**Nitrogen measured as nitrate and nitrite – N and ammonium-N

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Phosphorous levels in Wilson Inlet tended to be below the guideline value. The guideline values are an indication of the approximate phosphorous levels that may impact the health of an estuary.

The central deeper zone had phosphate levels above the guideline in the bottom layer when the bar was open. This was most likely due to the release of nutrients including phosphate from the sediments during very low oxygen (anoxic) conditions caused by stratification.

*Guideline is the ANZECC (2000) guideline value for south-west estuaries

** Phosphorous measured as filterable reactive phosphorous (phosphate – P)



Algae levels in Wilson Inlet were close to the guideline value for the bar closed period and two to three times higher than the guideline when open.

High algal activity during the bar open period corresponds to spring blooms, a typical feature of south west estuaries following high river inflows and warmer temperatures.

*Guideline is the ANZECC (2000) guideline value for south-west estuaries

** Algae measured as chlorophyll a Near Ocean = WI-30