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Water quality

The nitrogen cycle

Port Phillip Bay and Western Port have clean and healthy nitrogen cycles compared with similar bays close to population centres around the world.


Port Philip Bay is a ‘biologically’ dominated system – that is, it is dominated by phytoplankton.

By contrast, Western Port is a ‘biophysically’ dominated system – that is, it is governed by shore morphology, wave dynamics, wind and light.

Measuring the nitrogen cycle

Nitrogen fixation and denitrification are the critical nutrient cycle processes occurring in Port Phillip Bay and Western Port. Denitrification removes the food (nitrogen) from the system while fixation brings it in.

Denitrification efficiency

Denitrification efficiency (DE) is the proportion of recycled (metabolised) nitrogen lost to the atmosphere as nitrogen gas, compared with the total of inorganic nitrogen forms released by the microbial breakdown of organic matter. DE is estimated by measuring the movement between sediment and water column of the inorganic nitrogen forms – ammonium (NH4+) and oxidised nitrogen (NO2- and NO3-) – and comparing that with N2, which is created when organic matter decomposes in the sediment (see the infographic below, Nitrogen cycle in Port Phillip Bay).

High DE represents a system that effectively removes nitrogen that could potentially cause algal blooms, which can affect the health and recreational amenity of marine and estuarine waters.

nutrient cycling in Port Phillip Bay
Nutrient cycling in Port Phillip Bay. Image - Ou Design

Nitrogen fixation

Nitrogen enters the water through precipitation, runoff, or as N2 from the atmosphere. However, phytoplankton needs nitrogen in biologically available forms to synthesise organic matter. Therefore N2 must undergo nitrogen fixation, a process performed predominately by cyanobacteria (see infographic below, Nitrogen cycle in Western Port).

Nutrient cycling in Western Port. Image - Ou Design
Nutrient cycling in Western Port. Image - Ou Design
The nitrogen cycle in Port Phillip Bay

Nitrogen is an essential nutrient for the growth of marine life: the nitrogen cycle plays a key role in maintaining water quality. In Port Phillip Bay, it is denitrification that is the process which maintains water quality, removing Nitrogen from the system and releasing it into the atmosphere. How efficiently this is done is described as ‘denitrification efficiency' (DE). 

  • When DE is high, less nitrogen recycles and phytoplankton growth is limited.
  • When DE is low, phytoplankton proliferate, which leads to decreased water quality and the threat of algal blooms.

Levels of nutrients are monitored continuously under the Port Phillip Bay Environmental Management Plan (EMP). A new Port Phillip Bay EMP is being developed by Melbourne Water and DELWP and will be issued in 2017.

In 2002 the EMP established arrangements to detect changes in critical elements of nitrogen cycling in Port Phillip Bay to inform understanding of the cause of algal blooms, anoxia (absence of oxygen) and fish kills.

Climate change

Climate change may affect nitrogen cycling by an expected decrease in microphytobenthos (MPB) and an increase in plankton will possibly lead to algal blooms.

CSIRO’s climate change experts predict lower rainfall, increased evaporation, lower runoff, and increased storm events as a consequence of climate change. This indicates that baseline nitrogen loads from the catchment may decrease, but the frequency of floods may increase (up to 80% of nitrogen input into Port Phillip Bay is delivered during floods).

Delphinus delphis: common dolphin, image credit - David Donnelly, Dolphin Research Institute
Citizen science

If you love dolphins, you can help in their protection by joining in the Dolphin Research Institute’s Dolphin Watch program.

Your citizen science dolphin sightings are entered into a database that already contains hundreds of sightings dating back to 1993. The information allows DRI to identify important areas and if necessary, push for their protection. It may also lead to the identification of local issues or even wider threats that need to be addressed.

For more information, please read the case study on the Dolphin Research Institute.


Marine pests

Exotic fauna may affect nitrogen cycling by:

  • displacing or consuming the fauna living in the sediment which are important for enhancing denitrification, by pumping water through the sediment or by mixing freshly fallen organic matter deeper into the sediment.
  • intercepting organic matter before it reaches the sediment (short-circuiting denitrification); or
  • increasing nutrients in the water column by injecting wastes directly into the water column rather than into the sediment.

Impacts of exotic species on nutrient cycling have been demonstrated at small scales in Port Phillip Bay, though marine scientists are not aware of any documented cases elsewhere in the world where introduced marine pests have led to a system-wide collapse of nutrient cycling. 

What we know

Reductions in DE are likely following storm events, which may lead to acute short-term impacts (e.g. algal blooms, beach closures).

The Port Phillip Bay EMP includes an annual target for nitrogen in the bay, to keep the load well below levels that could risk eutrophication, but still support productivity for fisheries. There is high confidence that targets from the Western Treatment Plant (WTP) and the catchments have been met, based on weekly measurements of nitrogen in the discharges. 

What we need to know

Despite an increased understanding of nitrogen cycles in the marine environment,  further modelling and research is needed to identify the causes of stress observed in some habitats (e.g. seagrass and reefs).

Enhanced modelling of nutrient cycling processes is required:

  • to confirm that the generally high denitrification efficiency indicated by monitoring at two sites also applies at bay-wide and regional scales, and
  • to shift the focus in future EMPs from bay-wide and regional scales to a much finer, local scale, so that managers may be better informed of the varying scales of risk posed by nutrient inputs.

No event since 1994 has been large enough to lead to a decline in DE for more than a month, and even then only in a restricted area (Hobsons Bay).

Denitrification efficiency in Port Phillip Bay appears to be resilient to loads from the WTP and the catchments expected over the next 20 years. 

The nitrogen cycle in Western Port

Western Port is a shallow, well-flushed, significantly vegetated bay with a lot of light reaching the sediment. This means that there is both  seagrass and microphytobenthos (MPB), which have a high demand for nitrogen.

Western Port is generally considered to have low nutrient inputs relative to other bays such as Port Phillip Bay. It receives no direct sewage discharge, and the catchment inputs are comparatively small.


On average Western Port receives around 650 tonnes of nitrogen a year from the catchments, around 430 tonnes a year from nitrogen fixation and loses around 230 tonnes per year though denitrification.

Seagrass and nitrogen cycling

Seagrass represents one of the common types of vegetation found on tidal flats, and is a feature of Western Port. Seagrass can alter how nutrients such as nitrogen are cycled. In seagrass meadows nitrogen fixation is the dominant transformer of nitrogen into a nutrient.

Carbon is released into the sediment from the root system of the seagrass which increases activity of nitrogen fixing microbes, resulting in higher rates of nitrogen fixation. In addition, seagrass outcompetes nitrifying/denitrifying microbes which limits the loss of nitrogen through denitrification.

What we know

Nutrients do not pose the same level of risk in Western Port as they do in Port Phillip Bay because Western Port is a highly-flushed system with a shorter residence time of the water. That is, the nutrients that enter the bay as runoff from the catchments are spread across the large surface area of Western Port.

There is little denitrification in this environment, so nitrogen fixation governs the nitrogen cycle.

We measure the health of the nitrogen cycle in Western Port by monitoring the ratio of nitrogen fixation to denitrification.

What we need to know

In Western Port, the influence of vegetation and MPB on the net flux of nitrogen through the processes of denitrification and nitrogen fixation is not fully understood.

Western Port is dominated by tidal flats that are highly productive environments due to their large surface area, exposure to high light intensities and the presence of vegetation and/or MPB.

It is vital to understand how the balance of denitrification and nitrogen fixation in coastal ecosystems will respond to further reductions in seagrass coverage.


The Environmental Protection Authority (EPA) currently samples water quality monthly at eight sites in Port Phillip Bay and three sites in Western Port.

The range of indicators include:

  • nutrients (nitrogen, phosphorus and silicate)
  • water clarity (total suspended solids) and turbidity
  • salinity (salt)
  • dissolved oxygen
  • pH
  • metals (arsenic, cadmium, chromium, copper, lead, nickel and zinc)
  • algae such as chlorophyll-b and c and chlorophyll-a fluorescence, and plankton
  • harmful algae blooms (Port Phillip Bay only)
  • sediment contamination
  • water temperature, and
  • faecal contamination (Port Phillip Bay only).

There is mounting community concern about microplastics and the damage that it is doing to the marine environment, but for most of us we’re in the dark about how big the problem is and what we can to do to help. 

Port Phillip Bay

During the summer months,  water quality is reported daily on the Yarra & Bay website. The website issues alerts for;

  • pollution
  • fish death, and
  • algal blooms.

Beach Report monitors water quality at 36 Port Phillip Bay beaches, while Yarra Watch monitors water quality at four sites along the Yarra.

These programs have three broad objectives:

  • Provide information about beach water quality so the community can make informed decisions about swimming.
  • Identify trends in recreational water quality.
  • Strategically improve water quality.


What we know

Most beaches have met EPA’s objectives for swimming in recent years.

Over the last three summers most of the 36 beaches monitored in the bay (94-97%) have met objectives for swimming. 

Larus pacificus: Pacific gull
Citizen science

Join the Port Phillip Baykeeper in regular plastic pollution audits on streets and beaches; live mollusc surveys, and beach profiling.

Beach Patrol started as a push to clean Melbourne’s beaches using people power. But this dynamic organisation is constantly evolving. Fish around on the site and see the community inspired activities waiting for you to join.

Find out about how to help the battle against microplastics as part of  the EPA Victoria citizen science program.


Western Port

There are three long-term water monitoring sites in Western Port, located near Hastings, Barrallier Island and Corinella.

What we know:

Coastal erosion is a significant contributor to poor water clarity in some locations. In Western Port, high concentrations of sediments are detrimental to the aquatic ecosystem because it reduces the light available for photosynthesis. Sediment also carries other materials (toxicants, pathogens and organic matter)  that consume oxygen in the water column. Sediments from catchments and resuspension in Western Port settle out and smother seagrass and block light for seagrass growth.

What's the state of the water?

Despite their proximity to Victoria’s largest cities, Melbourne and Geelong, Port Phillip Bay and Western Port are quite healthy overall.

To measure the environmental health of the bays, the Commissioner for Environmental Sustainability worked with marine scientists who identified 36 indicators across the six key topics you see on this website.

The indicators were chosen because they best ‘indicate’ whether that key topic is healthy.

Here’s how water quality measured up:

Port Phillip Bay   Western Port  
Denitrification efficiency (DE) good Nitrogen fixation  good
Algae good Algae good
Water clarity good Water clarity poor
Salinity good Salinity good
Dissolved oxygen good Dissolved oxygen good
pH good pH good
Metals good Metals good
Harmful algae blooms fair Harmful algae blooms fair
Sediment contamination fair Sediment contamination fair
Temperature fair Temperature fair
Enterococci bacteria good Enterococci bacteria good