Port Phillip Bay Water Quality

ENVIRONMENT REPORT

PORT PHILLIP BAY WATER QUALITY

LONG- TERM TRENDS IN NUTRIENT STATUS AND CLARITY, 1984— 1999

ENVIRONMENT REPORT

PORT PHILLIP BAY WATER QUALITY

Long Term Trends in Nutrient Status and Clarity, 1984-1999

EPA Victoria 40 City Road, Southbank Victoria 3006 AUSTRALIA

January 2002

ISBN 0 7306 7611 0 Publication 806

OVERVIEW

Port Phillip Bay (the Bay) is of immense social, economic and environmental value to Victoria. Increased loads of nutrients, notably nitrogen (N), from the surrounding catchment are recognised as one of the major threats to the health of the Bay. The State environment protection policy (SEPP) Waters of Victoria Schedule F6 establishes a comprehensive policy framework for the protection of water quality in the Bay.

This report examines long-term trends in the nutrient status and water clarity of Port Phillip Bay from 1984 to 1999, and assesses compliance with defined environmental objectives for nutrient status and water clarity. Key findings from this study are discussed in the context of patterns of climate variation and human activities that may have contributed to variation in nutrient and sediment loads to the Bay.

EPA commenced approximately monthly sampling of water quality at three fixed sites in the Bay in 1984 and initiated sampling at a further 3 sites in 1990. Water samples are analysed for concentrations of the key nutrients — nitrogen, phosphorus and silicate — and chlorophyll, as an integrated measure of nutrient status. Secchi disk depth and suspended sediment are measured as indicators of water clarity.

During the 16 year dataset, the range of water column concentrations measured is dominated by pronounced inter-annual variability that is due to changes in climatic conditions, which in turn affects the amount of freshwater bearing nutrient and sediment to the Bay. Few long-term trends were detected during the entire dataset or applied Bay-wide. At no site were any of the SEPP environmental objectives met in all years. Nor was there any trend in compliance to indicate a long-term change in nutrient status or water clarity.

Trends that did occur were mainly at sites in the central and eastern parts of the Bay. Here, oxidized nitrogen concentrations decreased at one site, Central, from 1984 until 1999, and at two other sites, Patterson River and Dromana, from 1989 until 1995 when they were discontinued for logistical reasons. The reductions in nitrogen concentrations at these sites were not expressed in any consistent trend in chlorophyll concentrations. Phosphorus concentrations trended downward at Central, Dromana and Patterson River sites from 1989 until 1995, but subsequently have increased in concentration at Central, and Corio Bay sites. Water clarity improved at Central and Long Reef sites in the period 1989 to 1995 but has decreased in the subsequent four years.

On the western side of the Bay, Long Reef and Hobsons Bay are the two sites most heavily influenced by inputs of sediment and nutrient flowing from the Western Treatment Plant and the Yarra River. No long-term trends were detected at either of these sites and this is likely due to the influence of these nutrient sources. Although concentrations of nutrients were high at these two sites, compliance with environmental objectives for chlorophyll and Secchi disk depth were similar to other sites.

The nutrient status of the Bay appears to have altered over scales of two to five years, and this has resulted principally from changing climate conditions, rather than any significant change in human activities. Within the range of climate conditions experienced during this time, it would appear that the nutrient status and water clarity

i of the Bay has been maintained. Concentrations of the critical nutrient, nitrogen, have not increased over time and there is some evidence of a decrease.

This report is the first detailed analysis of data from EPA’s fixed site monitoring program. The findings reported here corroborate the findings and conclusions reached by the Port Phillip Bay Environmental Study2 (PPBES) that reported comprehensively on water quality conditions in the Bay from 1990 until 1995. Drawing together previous studies, the PPBES report concluded at the time that the Bay was in good “health”, and indicated that the nutrient status of the Bay had been maintained since routine monitoring commenced in the early 1980s. Some earlier data in the PPBES report indicates that it was probable that nitrogen levels had decreased since the early 1970s.

In the subsequent four years until 1999, the results reported here support and extend the conclusion that nutrient status and water clarity have continued to be maintained and that these patterns are largely the result of climate variation.

Reductions in nitrogen loads to the northwestern side of the Bay are expected with the implementation of a stormwater management program around the Bay and improved denitrification efficiencies at the Western Treatment Plant. With implementation of these actions it is expected that nitrogen loads will reduce progressively.

CONTENTS

OVERVIEW ...... I

INTRODUCTION ...... 1

ABOUT THIS REPORT...... 1

WHY MONITOR WATER QUALITY IN THE BAY? ...... 1

NUTRIENTS, CHLOROPHYLL AND WATER CLARITY ...... 4

METHODS ...... 8

WATER SAMPLING SITES ...... 8

DATA ANALYSIS AND INTERPRETATION ...... 8

NUTRIENT STATUS RESULTS...... 17

NITROGEN...... 17

PHOSPHORUS ...... 22

SILICATE ...... 26

CHLOROPHYLL A ...... 28

WATER CLARITY ...... 32

SECCHI DISK DEPTH...... 32

SUSPENDED SOLIDS...... 34

DISCUSSION ...... 36

HAS THERE BEEN A LONG-TERM IMPROVEMENT IN THE WATER QUALITY IN THE BAY?...... 36

HOW DOES WATER QUALITY IN THE BAY COMPARE WITH COMPLIANCE OBJECTIVES? ...... 38

CONCLUSIONS ...... 39

REFERENCES AND FURTHER READING ...... 41

REFERENCES ...... 41

FURTHER READING...... 42

APPENDIX 1. ANALYTICAL METHODS USED AND THEIR DETECTION LIMITS...... 43

GLOSSARY, ACRONYMS AND UNITS

Glossary

Anoxia: Absence of oxygen.

Anthropogenic: Involving human influence.

Beneficial Use: These are the uses that are protected in each segment. These are set out in more detail in Waters of Victoria (Schedule F6)1. In general terms beneficial uses are uses or values of the environment that are important for a healthy ecosystem or for public benefit, welfare, safety or health and which require protection from the effects of pollution.

Chlorophyll a: This photosynthetic pigment is found in all of the photosynthetic phytoplankton. It is used as an estimate of biomass.

Compliance: When the value for a particular parameter is below the environmental objective for that parameter.

Cryptophytes: A group of microscopic algae within the phytoplankton. Characterised by flattened cells, an oblique furrow and green, blue and red pigments.

Denitrification: An anaerobic process where nitrate is converted to nitrogen gas.

Diatoms: A group of microscopic algae that can be part of the phytoplankton. Characterised by an often ornate cell covering composed of silica.

Dinoflagellates: A group of microscopic algae that can be part of the phytoplankton. This group is conveniently divided into two subgroups. The first group is characterised by cells that have one flagellum in a longitudinal position and one in a transverse position. The second group is characterised by cells that are composed of two watch glass shaped halves and have two flagella that arise from the anterior part of the cell.

Environment Quality Objective: Targets for particular indicators that will ensure that the beneficial uses identified within each segment are protected.

Eutrophication: The process by which a waterway becomes enriched with nutrients. The nutrients involved are most commonly nitrogen and phosphorus.

Exceedance: When the value for a particular parameter exceeds the environmental objective or trigger value for that parameter.

Exchange rate: The rate at which water within a semi-enclosed waterbody is exchanged with ocean water.

Hypoxia: Any state where a physiologically inadequate amount of oxygen is available to, or utilised by tissue.

Indicator: A variable that is measured and interpreted to provide general information about the condition of an aquatic system.

Loads: Refers to the mass of a substance being added to a system and is a product of flow and concentration.

Mineralise: The process in which complex molecules are broken down into their constituents.

Nutrient Enrichment: The addition of nutrients particularly nitrogen and phosphorus.

PAR: Photosynthetically Active Radiation. This is the band of light with wavelengths between 400 and 700nm.

80th Percentile: The value which occurs in the 80th position when a group of numbers are arranged in ascending order.

Phytoplankton: A group of mostly photosynthetic microscopic algae that live free floating in the water column of rivers, lakes and oceans.

Primary Production: Production of organic matter using inorganic carbon, inorganic nutrients and light.

Red tide: This is a bloom of algae that causes a red surface scum. The causative organism is usually a dinoflagellate.

Residence time: The amount of time that a parcel of water spends in a semi-enclosed waterbody before it is transported to the open ocean.

Reference Site: A site that is not greatly influenced by human activity.

Secchi disk: a 30cm flat disk that is divided into alternating black and white segments. Used for measuring water clarity by lowering the disk through the water column until it is no longer visible.

Segment: A portion of Port Phillip Bay that has defined environmental objectives.

Sequester: The removal of dissolved nutrients from the water column.

Stratification: The division of a waterbody into two layers as a result of a vertical difference in salinity or temperature.

Trigger value: These are the concentrations of the key performance indicators measured for the ecosystem, below which there exists a low risk that adverse biological effects will occur. They indicate a risk of impact if exceeded and should ‘trigger’ some action, either further ecosystem specific investigations or implementation of management/remedial actions.

Type I error: Rejection of the tested null hypothesis when it is true.

Type II error: Accepting the tested null hypothesis when it is false.

Water clarity: This is the transparency of the water. This is affected by the amount of dissolved organic matter, suspended sediment and chlorophyll in the water.

Zooplankton: The animal portion of the plankton.

Acronyms

ANZECC: Australian and New Zealand Environment and Conservation Council

ARMCANZ: Agriculture and Resource Management Council of Australia and New Zealand

DIN: Dissolved inorganic nitrogen

DON: Dissolved organic nitrogen

DIP: Dissolved inorganic phosphorus

ENSO: El Nino Southern Oscillation

IP: Inorganic phosphorus

N: Nitrogen

NWQMS: National Water Quality Management Strategy

P: Phosphorus

PAR: Photosynthetically active radiation

PPBES: Port Phillip Bay Environmental Study

PSU: practical salinity units

SEPP: State environment protection policy

STP: Sewage Treatment Plant

TN: Total Nitrogen

TP: Total Phosphorus

WTP: Western Treatment Plant

WoV: Waters of Victoria

Units and prefixes g grams M Mega- 106 L litres k Kilo- 103 m metres c Centi- 10-2 mo month m Mill- 10-3 y year µ Micro- 10-6 % percent; parts per hundred = 10-2 n Nano- 10-9 ‰ Per mille, parts per thousand = 10-3 p Pico- 10-12 ppm parts per million = 10-6 f Femto- 10-15

INTRODUCTION Why monitor water quality in the Bay?

Port Phillip Bay is a large, shallow coastal About this report embayment that is of immense social, economic and environmental value to Victoria (Figure 1). However, This report summarises the results of water quality the many domestic, commercial and recreational monitoring undertaken in Port Phillip Bay (the Bay) activities on and around the Bay also put at risk the by EPA Victoria from 1984 to 1999. It assesses ecological health of the Bay. trends in the concentrations of key nutrients, amounts of phytoplankton as an integrated Increased loads of nutrients, notably nitrogen (N), measure of nutrient status, and water clarity. It also from the surrounding catchment are recognised as assesses compliance with defined environmental one of the major threats with the greatest potential objectives for nutrient status and water clarity. to invoke region-wide degradation of the health of the Bay (Box 1). Increased availability of the nitrogen Unfamiliar technical terms are highlighted in bold and phosphorus (P), and also silicate (Si), can and an explanation of their meaning can be found in stimulate the growth of plankton and macroalgae the glossary. For the more interested reader, with sometimes serious ecological and socio- citations to references are given as numeric economic consequences. superscripts, and text boxes provide additional information on key concepts and methods. A list of further reading is also given at the end of the report.

Figure 1. Port Phillip Bay showing the location of monitoring sites and some of the sources of nutrient and sediment that can affect the environmental quality in the Bay.

Physical features of Port Phillip Bay. Feature Amount Surface area 1930km 2 Maximum depth 24m Total volume 26km3 Catchment area 9790km2

Box 1: Effects of Nutrient Enrichment and the susceptibility of coastal ecosystems.

The introduction of excess nutrients into coastal systems, or nutrient-enrichment, has a number of impacts. One of the most common effects is acceleration of a natural process known as eutrophication – that is, the increasing enrichment of an ecosystem with organic material that is formed by primary productivity (that is, photosynthetic activity). In moderation, increasing organic matter can sometimes be beneficial, such as when an increased rate of primary production leads to greater fishery production. Far more often, however, eutrophication is stimulated to harmful levels by the anthropogenic introduction of high concentrations of nitrogen and phosphorus. This can result in a variety of negative impacts including: excessive, and sometimes toxic, production of algal biomass; loss of important nearshore habitat such as seagrass beds (caused by light reduction); changes in marine biodiversity and species distribution; increased sedimentation of organic particles; and depletion of dissolved oxygen (hypoxia and anoxia). Furthermore, these effects can cause adverse impacts further up the food web. For example, red tides and hypoxia can cause fish kills. Similarly, red tides and blooms of other toxic algae can harm marine mammals. It is important to note that eutrophication (effect) is only one of many possible responses of coastal ecosystem can have to nutrient over-enrichment (cause). For example, changes in the relative concentration of certain nutrients may trigger adverse changes in the relative abundance of some species without triggering an overall increase in primary productivity.

The susceptibility of estuaries and coastal systems to accelerated nutrient inputs varies due to a number of physical factors. The volume and depth of a waterbody, as well as the size, and landuse and elevation of the surrounding catchment are important factors determining the areal nutrient loading. Perhaps the most important factor determining susceptibility is the amount of exchange between the water body and the open ocean (which results in a reduced residence time for the nutrients to be taken up by local biota). Thus water bodies with low exchange rates with the ocean seem to be particularly vulnerable. Stratification, caused by poor flushing, high water temperatures or the intrusion of saltwater under freshwater can also be important. Other biological factors such as community structure, the proportion of phytoplankton grazed, the rates of denitrification and nitrogen fixation can also be important.

To sustain the opportunities the Bay provides—now of water quality in the Bay (Box 2). Beneficial uses and for future generations—the activities on and are the basis for maintaining environmental quality, around the Bay that threaten the biodiversity and and environmental quality objectives are set to ecological processes that operate within the Bay, ensure the protection of designated beneficial uses. must be managed. The objectives provide targets for particular indicators of the condition of the Bay’s The State environment protection policy (SEPP) environments. Within the Bay, six segments are Waters of Victoria Schedule F6 establishes a recognised that reflect the different types and comprehensive policy framework for the protection

conditions of environments and community values rivers, most notably the Yarra, smaller streams, requiring protection (Box 2 and Figure 1). about 350 storm water drains, and two sewage treatment plants (STPs) — Werribee Treatment plant EPA Victoria has been monitoring the water quality (WTP) and Altona (Figure 1 and Box 3). Groundwater of Port Phillip Bay since 1984. The aim of this discharge into the Bay is considered insignificant. monitoring is to determine if there are any long-term trends in the water quality of the Bay, to assess the Within the Bay, nutrient and sediment general condition of the Bay and to assess the concentrations can vary greatly. Spatially, success of management actions through the concentrations are usually greater inshore or compliance with environmental objectives. adjacent to major inputs.

Nutrients, chlorophyll and water clarity

Inputs or loads of freshwater, nutrient and sediment to the Bay are reasonably well understood (Box 3). These inputs enter the Bay principally from several

Box 2: Water Quality Management Policies

State environment protection policy Waters of Victoria F6

Waters of Victoria (WoV) Schedule F61 declared in 1997 is a comprehensive policy framework for the protection of water quality in the Bay. Beneficial uses are the basis for maintaining environmental quality. In marine waters they are: (1) maintenance of natural aquatic ecosystems; (2) water based recreation; (3) production of molluscs for human consumption; (4) commercial and recreational use of edible fish and crustacea; (5) industrial water use; and (6) navigation and shipping.

Within the Bay, six segments, or regions, are recognised. These reflect the different types and conditions of environments, different surrounding landuses and major inputs. These segments have different beneficial uses requiring protection (Figure 1):

Hobsons Segment: includes the mouth of the Yarra River and the city of Melbourne and its Port facilities.

Werribee Segment: the part of the Bay adjacent to the WTP outfalls.

Corio Segment: All waters in Corio Bay.

Inshore Segment: covering all waters within 600m of low tide. This segment corresponds to the region of greatest impact.

Aquatic reserves: those parts of the Bay afforded statutory protection.

General Segment: all other waters in the Bay. These are considered to be least affected by catchment practices.

Environmental quality objectives are set for each segment to ensure the protection of designated beneficial uses. The objectives provide targets for particular indicators of the condition of the Bays environments. The key indicators for nutrients are not nutrient concentrations but chlorophyll a because it is considered an integrative measure of nutrient status. For water clarity, Secchi disk depth and PAR attenuation are used. Specific objectives are set for each segment and are shown in Table 3. As nutrient and sediment objectives are not set in the SEPP, the National Water Quality Management Strategy Guidelines3 values and approach are used to assist interpretation (see Box 7).

Recognising the importance of nitrogen as the key nutrient affecting the health of the Bay, the SEPP sets a 1000 tonne reduction in nitrogen loads to the Bay.

Water exchanged with Bass Strait through a narrow In Port Phillip Bay it is now well understood that gap (Figure 1) can also influence concentrations of nitrogen is the nutrient primarily controlling the nutrient and sediment. Exchange rates in the Bay extent of eutrophication2. Denitrification is a key are low, on average about one year12, but are less at process ensuring the removal of nitrogen and the the southern end of the Bay close to the entrance to maintenance of the ‘ecological health’ of the Bay. Bass Strait. In Corio Bay the exchange rate is about Nitrogen occurs in dissolved organic (DON), 16 months as a sand bar on the eastern side of Corio inorganic (DIN) and particulate forms that together Bay restricts exchange with the Bay. The low comprise total nitrogen (TN). DIN concentrations exchange rates that occur in the Bay have important comprise less than 10 per cent of TN. implications for the cycling of nutrients in the Bay Concentrations of phosphorus in the Bay are high (Box 1). relative to other enclosed coastal water bodies and As the Bay is relatively shallow, water in the Bay is are comprised principally of dissolved inorganic generally vertically well mixed. Stratification occurs orthophosphate (DIP). in Hobsons Bay following significant water flow in Chlorophyll a is a crude measure of phytoplankton the Yarra River and occasionally in the deeper abundance (Box 4). It is used as an integrated central Bay area during summer. measure of nutrient status. Chlorophyll a varies Nutrients enter the Bay in particulate and dissolved around the Bay primarily in response to the forms that include organic and inorganic availability of nitrogen that stimulates compounds. Dissolved inorganic forms are the types photosynthetic activity. Chlorophyll a concentrations of nutrients that are most readily available to are higher in waters close to shore and in areas phytoplankton. Complex forms of nutrients can be adjacent to the Yarra River and the WTP. broken down in the water column by bacteria and The expressed result of nutrient loads is a function zooplankton, and in the sediments primarily by of the geography of the Bay, the position of the bacteria. inputs, and the wind-driven circulation of water

masses in the Bay. Nutrients entering the Bay will be and chlorophyll contribute to water clarity. Previous assimilated close to shore. Phytoplankton blooms studies in the Bay have established that suspended will usually occur before nutrients can be mixed solids and chlorophyll together are responsible for offshore. Thus the main impact of nutrient load is less than half (18 to 43 per cent) of the observed restricted to nearshore waters. attenuation in photosynthetically active radiation (PAR).6 It appears that Bay water has a significant Water clarity is essential for phytoplankton growth intrinsic attenuation perhaps due to dissolved and benthic algal growth. Both suspended solids organic matter.

Box 3. Annual nutrient and inputs to the Bay

Knowledge of nutrient inputs to the Bay is essential in interpreting long-term changes in the concentration of these parameters in the Bay. There can be considerable seasonal and interannual variation in nutrient loads. Although monitoring is interested primarily in distinguishing changes in base-flow nutrient inputs (for example, changes landuse practices) it is necessary to consider these trends in the context of climatic variation. Changes in rainfall alters the timing and magnitude of the delivery of nutrients and sediment to the Bay. Changes in weather patterns may also result in differences in the vertical and horizontal mixing of water masses in the Bay and may invoke changes in the rates of transformation processes such as biological assimilation and denitrification.

Table 1 summarises a nutrient budget of the major nutrient inputs to the Bay. The average annual N input to the Bay is about 7000 tonnes per year (t y-1), and phosphorus loads are about 2000 t y-1. The Yarra River and the WTP are the principal sources of nutrients to the Bay, together accounting for 78 per cent of the N and 73 per cent of the P discharged to the Bay every year.

Table 1. Mean annual loads (t y-1) of nitrogen (N), phosphorus (P) to the Bay from major sources compiled from several sources 6,

TN TP WTP 3667 940 Yarra River 1822 668 Other* 1640 380 Total 7129 1988 * Includes rivers, streams and drains

Box 4. Nutrient and water clarity parameters explained

Nutrients

Nitrogen: Nitrogen is the key nutrient determining the rate of primary production in marine ecosystems, including Port Phillip Bay. Dissolved inorganic nitrogen (DIN) in the form of nitrate, nitrite and ammonia are most readily used by phytoplankton for photosynthesis. The dominance of the major inorganic nitrogen species varies among sources and can vary seasonally. Nitrate is the dominant N compound discharged from rivers. Ammonium is the major N compound discharged from WTP. Nitrogen is also removed from the Bay as N2 by denitrification and this is a critical process maintaining the health of the Bay.

Phosphate: Phosphorus is required by phytoplankton for growth and may under some circumstances limit the rate of primary production. Orthophosphate is the form of phosphorus most readily available to phytoplankton. Concentrations in the Bay are naturally higher than many other places but are not a threat to marine ecosystem health. Monitoring over 30 years shows P concentrations have remained essentially unchanged.

Silicate: The availability of silicate in a waterbody has little or no influence on the overall rate of primary production but influences the composition of phytoplankton. When silica is abundant, diatoms are one of the major components of the phytoplankton; when silica is in low supply, other classes dominate the phytoplankton composition. Inputs of biologically available silicate come largely from the weathering of soils and sediments.

Chlorophyll a: Chlorophyll a is a crude measure of phytoplankton abundance but provides no indication of taxonomic distribution. As phytoplankton are primarily limited by nutrient availability, chlorophyll a is often used as a integrated surrogate measure of nutrient status. There are about 230 species of phytoplankton identified in the Bay. Diatoms dominate (62 per cent) as silica is relatively abundant in the Bay, while other important groups include cryptophytes (8.5 per cent) and dinoflagellates (7.3 per cent)5.

Water Clarity

Suspended Solids: Inorganic and organic particulate material suspended in the water column cause turbidity and decrease water clarity. It is measured by filtering a water sample through a glass fibre filter (nominally 0.7mm pore size).

Secchi Disk Depth: This is the depth at which a Secchi Disk is no longer visible when lowered through the water column.

METHODS Sampling commenced in 1984 at three of the sites and is continued to present. In 1990 sampling began at the another three sites, but due to logistical Water Sampling Sites constraints two of these were discontinued in 1996. The EPA has sampled water quality approximately monthly at six fixed sites in the Bay (Table 2).

Table 2. Sampling period and locations. Latitude and longitude given in decimal degrees.

EPA Location Segment Lat Long sampling No.

1229 Central General 38.0586 144.5916 1984–99 136 1282 Dromana General 38.3050 144.9900 1990–96 49 1911 Corio Bay Corio 38.1026 144.3974 1984–99 131 1991 Hobsons Bay Hobsons 37.8718 144.9325 1984–99 135 0369 Long Reef Werribee 38.0308 144.5916 1990–99 77 0969 Patterson River Inshore 38.3050 144.9900 1990–96 48

Two sites, Central and Dromana, (Figure 1) are · Long Reef is located approximately 1km from the nominally considered to be reference sites for the WTP. purpose of calculating nutrient and suspended · Pattersons River is located about 300m from sediment trigger values (see Box 6). These sites are shore and to the south of Patterson River. distant from catchment sources of nutrient and · Corio Bay is close to domestic and industrial sediment and are not directly influenced by any one inputs to Corio Bay. source. Undoubtedly, concentrations of nutrient and sediment at these sites will reflect cumulative Bay- Each of these sites are located in specific SEPP wide changes in water-quality resulting from human segments and are considered to be representative of activities; however inter-annual variation is more those segments (Table 2). likely to reflect natural variation rather than direct Single water samples are collected unfiltered from catchment inputs. about 0.5m below the surface and stored for later The other four sites are likely to be directly analysis. Nutrient and water clarity parameters influenced by various human activities such as measured and their meaning are given in Box 4. The sewage or riverine discharge (Figure 1). analytical methods used are in Appendix 1.

· Hobson Bay is approximately 800m from shore Data analysis and interpretation and is primarily influenced by discharge from the Yarra River. Data analysis evaluated trends in nutrient status and water clarity indicators from 1984 to 1999 with the following questions in mind:

· Long term trends: Is there a discernible long- to the variability that is a common feature of this term trend at each site? Are temporal patterns type of data. The analysis techniques are described consistent at broader regional scales? in more detail in boxes 5, 6 and 7.

· Compliance: Do the annual median values at In the results section, analyses of nitrogen, individual sites meet SEPP objectives for phosphorus and silicate, chlorophyll, suspended nutrient status and water clarity, or defined solids and Secchi disk depth are discussed. For trigger values? each indicator, at each site, graphs (Figures 4 to 10, 12, 13) present the annual median concentrations These analyses were broadly interpreted in relation bracketed by error bars of the 95% confidence to known patterns of nutrient and sediment inputs intervals. Confidence intervals reflect the amount of to the Bay. It was also examined if these patterns intra-annual variation associated with each annual may have resulted from human activities or were the median. The amount of variation differs for each result of natural variation. Where there were data parameter and differs among sites. The SEPP available, analysis examined whether there were environmental objective, or the trigger value, is discernible relationships with nutrient and sediment shown on graphs. load data. Other indirect proxies such as salinity and suspended sediment load were also used to Summary statistics and the results of any major examine if such relationships existed. trends are given in Tables 5 and 6.

Although there are a variety of ways in which the Figure 11 shows the percentage compliance with data can be evaluated, annual median values (the environmental objectives for chlorophyll and Secchi 50th percentile) were used as this statistic is robust disk depth.

Box 5. Data analysis techniques

Data Screening: In the 1980s there were a number of changes in the methods of chemical analysis and the analytical detection levels possible with the current technology. This caused problems for the statistical analysis and interpretation of these data. As a result most, but not all, data from the entire sampling periods have been analysed. Data that were not normally distributed were log-transformed. In some cases extreme outliers were excluded from the analysis.

Summary statistics: Annual medians were used for presentation of data in the figures, and for assessment of compliance.

Confidence intervals: Non parametric 95 per cent confidence intervals were calculated for each median8 and show the amount of uncertainty around whether the median is a robust measure. Where there were less than six samples, a confidence interval could not be calculated and only the median is shown. Confidence intervals reflect the amount of intra-annual variation associated with each annual median. The amount of variation differs for each parameter (for example, compare ammonia and orthophosphate) and differs among sites.

Those sites closely associated with a putative sources often show large amounts of intra-annual variation because of the short-term influences of these inputs.

Data exploration and long-term trends: Annual median values were used to assess long-term trends. Runs tests were conducted as an exploratory tool to discern whether there were systematic temporal patterns in the annual median such as mixtures, clusters, cycles and trends9. To minimise Type II errors, runs tests were evaluated with a Type I error rate set to = 0.1. Where patterns were detected in the annual data, further analysis was undertaken to establish whether there were coherent patterns in the monthly data. Regression models were used to model the outcome variable in terms of explanatory variables (see box 7). This method accommodates serial dependence (that is, autocorrelation) in the error. Together with seasonal adjustment a variety of polynomial terms were evaluated to best ‘model’ the observed data.

Box 6. Assessing compliance with SEPP Environmental Objectives:

For the 6 segments in the Bay (Box 2) the SEPP defines specific environmental objectives for chlorophyll, as an integrated measure of nutrient status, and Secchi disk depth as an indicator of water clarity (Table 3).

Table 3. SEPP Environmental Objectives for Chlorophyll and Secchi Disk depth in Port Phillip Bay.

Corio Hobsons Werribee Inshore General Chlorophyll a (µg L-1) annual median 1.5 2.5 2.5 1.5 1.0 annual 90%ile 2.5 4.0 4.0 2.5 1.5 Secchi Disk Depth (m) Annual median > 3 > 2 >3 >3 >4

Assessing whether these objectives are being met is essential for the ongoing management of the Bay, but is often complicated by limitations of sampling and the intrinsic variation that occurs as a result of seasonal processes as well as longer-term climate variation. The approach most commonly used and given in the SEPP is to compliance assess the median or percentile value and ignore the confidence intervals.

In this document confidence intervals have been considered explicitly in the compliance assessments.

Annual compliance was assessed by expressing the number of times the environmental objective was not met. Four categories were used that incorporated the degree of certainty with which it could be correctly concluded that compliance was met:

1. If the median value was below the environmental objective then it was assumed compliance was met and it was “passed”.

2. If the median and the upper confidence interval was below the objective then an “unambiguous pass” was given.

3. If the median and the lower confidence interval was above the objective then an “unambiguous fail” was given.

4. If confidence intervals spanned the environmental objective, or if there was not sufficient data to develop a confidence interval (a minimum of six samples are need to calculate an annual 95 per cent confidence interval), the result was classified as either an “ambiguous pass or fail”, depending on where the median was above or below the objective.

Box 7. Developing regional nutrient and sediment trigger values

As no environmental objectives for nutrients and suspended sediment are set in the SEPP, regional trigger values were derived as recommended in the ANZECC National Water Quality Management Strategy Guidelines (2000). In this approach reference sites are used to develop trigger values which are then used to benchmark other sites that are affected by human activities. Trigger values—as the name suggest—may initiate further monitoring or evaluation if they are exceeded. Unlike the environmental objectives they cannot be used to assess compliance.

For each nutrient parameter, data from the Central and Dromana reference sites were pooled and the 80th percentile of the data was calculated to derive the reference trigger values shown in Table 4.

Table 4. ANZECC3 and regionally derived nutrient trigger values (mg L-1). Note the regional triggers are based on the 80th percentile but are rounded to the nearest whole number. N/A, not available.

Regional trigger value NQWMS No. samples Median Trigger Default value Inorganic Phosphorus 184 61.3 67 5 Total Phosphorus 184 72.8 79 30 Oxidized Nitrogen 132 0.4 0.7 15 Ammonia 159 5.2 7 15 Total Nitrogen 139 169.5 161 300 Silicate 184 139.7 184 N/A Suspended Solids 147 2.40 3 N/A

National default trigger values are also shown. It is clear, notably for phosphorus, that the national default trigger values are inappropriate and that reference triggers should be developed wherever there is sufficient data available for a site that can be considered a suitable reference.

Box 8. Explaining the patterns

Knowledge of nutrient inputs to the Bay is essential to interpreting long-term changes in the concentration of these parameters in the Bay. It is necessary to distinguish changes in base-flow nutrient and sediment inputs (for example, changes in landuse practices) from climatic variation. Changes in rainfall alters the timing and magnitude of the delivery of nutrients and sediment to the Bay.

It has not been possible to calculate riverine nutrient loads for all years in the period 1984 to 1999 because of the lack of nutrient concentration and flow data and because the relationships between freshwater flow and concentration is not always straightforward. Instead, several proxies of riverine input were used to qualitatively interpret monitoring results. Patterns in annual rainfall (Figure 2) show how freshwater discharges to the whole Bay vary from year to year. Notably 1997 to 1999 were ‘drier’ than average while 1991 to 1993 were ‘wetter’ than average.

Figure 2. Mean annual rainfall across Port Phillip Bay. Data are the annual average rainfall summarised from Bureau of Meteorology stations at Melbourne, Queenscliff, Mornington and Dromana.

As salinity is measured concurrently with other water quality parameters it was used as a robust proxy for freshwater inputs, either from riverine inputs or as direct rainfall. Suspended solid concentrations can be another indicator of riverine input. Regression analyses were carried out to assess the contribution of salinity and suspended sediment in explaining the observed patterns in the dependent variables. Coefficients of determination (R2) from these analyses indicate the proportion of variation explained by the explanatory variable.

Box 9. Discharges from Western Treat Plant

WTP is the greatest source of nutrients to the Bay (Box 3). Detailed records for monitoring were available and are plotted in the figures below. Yearly variation is principally due to variation in rainfall and water flow. Total nitrogen loads are about 3000 t y-1 varying over the period from 2809 to 4502 t y-1. Nitrogen loads are comprised primarily of ammonia and this proportion has increased in recent years. Phosphorus loads have increased in recent years.

Suspended solid loads have decreased in recent years.

Figure 3. Annual discharges loads from WTP of nitrogen (A) phosphorus (B) and suspended solids (C).

Table 5: Overall summary statistics for the nutrient status and water clarity parameters.

Overall summary statistics Compliance / non- exceedance N Median Range 20%-ile 80%-ile Objective / % trigger value Inorganic Long Reef 77 121 59.8–696 86.8 204 67 0 Phosphate Pattersons River 48 67.6 40.2–124 59.5 81.4 67 43 (mg L-1) Central 135 62.7 9.8–117 56.1 70.5 Dromana Bay 49 56 32.976.3 47.9 63.1 Corio 131 90.1 63.4–190 78.8 102 67 0 Hobsons Bay 135 76.1 22.6–129 64.7 91.0 67 6 Total Long Reef 77 136 76.7–992 102.7 243 79 0 Phosphorus Pattersons River 48 83.8 66.5–158 73.2 92.6 79 43 (mg L-1) Central 135 75.3 45.8–137 68.2 83.2 Dromana Bay 49 66 46.4–86.6 57.2 72.1 Corio 131 106 84.8–221 94.7 119 79 0 Hobsons Bay 135 95. 1 58.9–162 83.1 112 79 6 Ammonia Long Reef 77 17.7 1.8–1496 5.2 160 7 0 (mg L-1) Pattersons River 48 5.6 0.4–151 3.4 13.5 7 71 Central 107 5.0 0–33.8 3.1 7.2 Dromana Bay 49 5.3 0.1–15.6 2.5 6.1 Corio 102 6.5 0.9–141 4.3 10.3 7 50 Hobsons Bay 107 6.8 0.2–102 4.14 14.3 7 43 Oxidised Long Reef 77 5.0 0–324 0.6 46 0.7 0 Nitrogen Pattersons River 46 2.1 0.2–249 0.3 11.3 0.7 43 (mg L-1) Central 87 0.3 0–8.7 0 0.9 Dromana Bay 45 0.6 0–20.9 0.3 1.0 Corio 90 0.9 0–20.9 0.2 3.0 0.7 46 Hobsons Bay 90 7.9 0–175 0.6 37.2 0.7 0 Total Long Reef 77 280 145–3083 203 493 161 0 Nitrogen Patterson River 48 175 119–501 157 217 161 0 (mg L-1) Central 90 156 129–199 143 169 Dromana Bay 49 153 101–192 136 171 Corio 90 209 157–374 189 236 161 0 Hobsons Bay 90 221 175–469 190 269 161 0 Silicate Long Reef 77 141 8.0–431 73.3 209 184 80 (mg L-1) Pattersons River 48 189 7.2–682 86.5 302 184 29 Central 135 134 1.9–424 49.3 241 Dromana Bay 49 155 3.1–271 67.3 226 Corio 131 120 0–517 67.3 214 184 69 Hobsons Bay 135 232 20–1645 113 385 184 19 Chlorophyll a Long Reef 77 1.6 0.4–14.1 1.0 3.6 2.5 0 (mg L-1) Pattersons River 48 1.0 0–8.8 0.61 2.1 1.5 14 Central 130 0.8 0–2.5 0.5 1.2 1.0 Dromana Bay 48 0.6 0–5.0 0.4 0.8 1.0 Corio 126 0.9 0–5.1 0.6 1.3 1.5 47 Hobsons Bay 129 2.0 0.4–10.5 1.1 3.3 4.0 0 Secchi depth Long Reef 77 4.3 1.3–7.0 3.12 5.18 3 100 (m) Pattersons River 48 2.5 1.0–9.5 2.32 6.0 3 43 Central 131 6.0 2.7–15.0 4.9 8.25 4 94 Dromana Bay 49 4.5 2.2–8.0 4.0 5.6 4 100 Corio 126 4.5 1.9–7.5 3.5 6.0 3 100 Hobsons Bay 130 3.0 1.0–6.3 2.2 4.22 2 88 Suspended Long Reef 76 3.8 0.7–19.9 1.9 5.8 3.3 40 Solids Pattersons River 48 2.5 0.2–11.2 1.3 4.5 3.3 71 (mg L-1) Central 98 2.7 0.31–12.8 1.3 4.2 70 Dromana Bay 49 2.0 0.2–6.0 0.9 3.1 100 Corio 92 3.2 0.8–12.4 2.0 4.2 3.3 58 Hobsons Bay 98 4.0 1.1–16.7 3.0 6.0 3.3 25

Table 6. Summary of significant trends tests using monthly data. The period over which trends were either significantly downward (-ve) or upward (+ve) and the number of years over which the trend was significant are indicated.

Site Ammonia Oxidised Nitrogen Inorganic Total Phosphorus phosphate Central -ve 1989-99 -ve 1989-1996 +ve 1996-99 +ve1996-1999 Dromana -ve 1989-96 -ve 1989-1996 -ve 1989-96 Patterson R. - ve 1990-96 -ve 1989-96 -ve 1989-96 Corio Bay -ve 1989-99 +ve 1996-99 +ve 1996-99 Hobsons Bay Long Reef

Table 7. Summary of compliance with SEPP objectives incorporating confidence intervals. The annual median for chlorophyll and Secchi disk depth at each site were either passed or failed. Incorporating the 95 per cent confidence interval each pass/fail classified “unambiguous” if the confidence interval was contained within the objective. It was classified as “ambiguous” if either the confidence interval spans the objective, or if no confidence intervals can be calculated (see Box 6) The number of ambiguous cases are not reported in the table below.

Central Corio Hobson Long Dromana Patterson Bay Reef River No of years 16 15 16 10 7 7 Median Chlorophyll Passed Median 14 13 12 9 7 4 Unambiguous 5 10 1 2 3 2 Failed Median 2 2 4 1 - 3 Unambiguous 0 0 0 0 - 0 Secchi disk depth Passed Median 15 15 16 10 7 3 Unambiguous 12 9 6 3 4 0 Failed Median 1 - - - - 4 Unambiguous 1 - - - - 4

NUTRIENT STATUS RESULTS less than 10mg L-1, 8mg L-1 and 250mg L-1 respectively (Figures 4, 5 and 6).

Nitrogen Both ammonium and oxidised nitrogen concentrations showed a steady downward trend in Reference sites: Overall median total nitrogen median concentration between 1990 and 1996 concentrations were similar at Dromana Bay (Table 6, Figures 4 and 5). (153mg L-1) and Central (156mg L-1) sites and a trigger value of 161mg L-1 was derived (Table 4). DIN Both ammonium (R2 = 0.18) and oxidised nitrogen concentrations comprised less than 4 per cent of (R2 = 0.37) were negatively related to salinity. The total nitrogen concentrations and were dominated strong relationship that occurs between oxidised by ammonium (Table 5). Overall median nitrogen and salinity is essentially due to high concentrations of ammonium and oxidised nitrogen oxidised nitrogen concentrations always occurring at at Dromana Bay (5.3, 0.6mg L-1) and Central (5.0, salinities less than 32 PSU. At salinities greater than 0.3mg L-1) sites were similar (Figures 4 and 5). Trigger 32 PSU, oxidised nitrogen concentrations were less values of 0.7 and 7mg L-1 were calculated (Table 4). than 10mg L-1. Oxidised nitrogen was also positively related (R2 = 0.18) to suspended solids At Dromana Bay there was a downward trend in concentrations. ammonium between 1989 and 1996 (Table 6). Similarly, at Central ammonium concentrations For the six years of data, ammonium and oxidised trend downward between 1989 and 1999. nitrogen concentrations fell below the reference trigger value in 71 per cent and 43 per cent of cases Corio Bay: Overall median ammonium and oxidised respectively (Figures 4 and 5). All total nitrogen nitrogen concentrations were 6.5mg L-1 and 0.9mg L-1 annual medians exceeded the reference trigger respectively (Table 5). Overall median TN value. Each value for all nitrogen species was below concentration for the period was 209mg L-1. the default national trigger value. There was a downward trend in oxidised nitrogen Hobsons Bay: The overall median ammonium concentrations between 1989 and 1999 (Table 6). concentrations was 6.8mg L-1. The overall median Ammonium and oxidised nitrogen concentrations concentration for oxidised nitrogen was 7.9mg L-1 and were below the reference trigger values about 50 per this was the highest overall median concentration cent of the time but TN concentrations were always recorded for Port Phillip Bay (Table 5). The overall above the reference trigger value. median TN was 221mg L-1. Annual median Patterson River: The overall median concentrations concentrations of ammonium and oxidised nitrogen -1 of ammonium and oxidised nitrogen were 5.6mg L were generally less than 10mg L-1 (Figures 4 and 5). -1 and 2.1mg L . The overall median TN concentration Annual median concentrations of total nitrogen were -1 was 175mg L . generally between 200mg L-1 and 250mg L-1 (Figure 6). Annual median concentrations of ammonium, oxidised nitrogen and total nitrogen were generally

At the Hobsons Bay site oxidised nitrogen concentrations of oxidised nitrogen occurred concentrations (R2 = 0.37) were negatively correlated between May and August. This is consistent with the with salinity. pattern of discharge of nitrogen from WTP.

For the 15 years of data ammonium concentrations On no occasion did the annual medians of fell below the reference trigger value 43 per cent of ammonium, oxidised nitrogen or TN fall below the the time but on no occasions did oxidised nitrogen reference trigger values. On two occasions in the 10 or TN annual medians fall within the reference years of data annual median concentrations of trigger value. Annual median ammonium and total ammonium and oxidised nitrogen have breached nitrogen concentrations fell below the national the national trigger values. Total nitrogen trigger value on all occasions. The annual median concentrations have breached the national trigger oxidised nitrogen concentrations were below the on four occasions during this period. national trigger value in 73 per cent of cases.

Long Reef: Overall median concentrations of ammonium, oxidised nitrogen and total nitrogen were 17.7mg L-1, 5mg L-1 and 280mg L-1 (Table 5). The values recorded for ammonium and total nitrogen were the highest overall medians recorded for the Bay. The value recorded for oxidised nitrogen was the second highest overall median recorded for the Bay. The annual median concentrations of ammonium were highest at Long Reef with peak values being recorded in 1990, 1996 and 1998 (Figure 4). Annual median concentrations of ammonium and oxidised nitrogen were generally less than 20mg L-1 and 10mg L-1 respectively (Figures 4 and 5). Annual median total nitrogen concentrations were generally 250mg L-1 or greater (Figure 6). Variation of individual measurements for all nitrogen species, as shown by the confidence intervals, is much greater at Long Reef than at the other sites.

The annual median ammonium concentrations at Long Reef were always higher than the reference trigger value (Figure 4). At Long Reef higher concentrations of ammonium and TN occurred between May and October while higher

Figure 4. Ammonium. Annual median concentrations (µg L-1) at reference and assessment sites. Error bars are the 95 per cent confidence intervals. The reference trigger value calculated from pooled reference site data is shown as a red line. The NWQMS national default trigger value is shown as a green line.

Figure 5. Oxidised Nitrogen. Annual median concentrations (µg L-1) at reference and assessment sites. Error bars are the 95 per cent confidence intervals. The reference trigger value calculated from pooled reference site data is shown as a red line. The NWQMS national default trigger value is shown as a green line.

Figure 6 Total Nitrogen. Annual median concentrations (µg L-1) at reference and assessment sites. Error bars are the 95 per cent confidence intervals. The reference trigger value calculated from pooled reference site data is shown as a red line. The NWQMS national default trigger value is shown as a green line.

Phosphorus were no significant relationships between DIP or TP and salinity and/or suspended solids. Reference sites: At the Central and Dromana sites, long-term overall median for the period Only 6 per cent of annual median DIP concentrations concentrations of IP were 63mg L-1 and 56mg L-1 fell below the reference trigger value and on no respectively (Table 5) and of TP were 75 and 66mg L-1 occasions did TP concentrations fall below the respectively. Interannual variability is however reference trigger value. The reason is likely to be the significant but the two sites closely track each other. longer residence time of water in the Corio Arm of the Bay. Annual median DIP concentrations at the reference sites were between 50mg L-1 and 70mg L-1 (Figure 7). Patterson River: the overall median concentrations Annual median TP concentrations were between of DIP and TP were 68 and 84µg L-1 respectively, 60mg L-1 and 90mg L-1 (Figure 8). At the Dromana site which are the lowest overall median for the periods there was a downward trend in annual medians and recorded for the assessment sites. Annual median monthly data of DIP and TP between 1989 and 1996 concentrations of IP are between 60mg L-1 and 90mg (Figures 7 and 8). At the Central site there was little L-1 and for TP concentrations are between 70mg L-1 change during most of the sampling period but and 100mg L-1. concentrations of both phosphorus species There was a decline in annual medians and monthly increased between 1996 and 1999 (Figures 7 and 8). concentrations between 1989 and 1996 for both DIP This increase was associated with an increases in and TP (Figures 7 and 8). These patterns were salinity with DIP concentrations generally positively consistent with decreases in phosphate related (R2 = 0.28) to salinity. concentrations also recorded at the Dromana Bay site. TP was positively related (R2=0.18) to The derived reference trigger values for DIP and TP suspended solid concentrations. are 67 and 69µg L-1 respectively. The concentrations are far greater than the recommended ANZECC3 The Patterson River site had the highest level of trigger because phosphorus has accumulated in the compliance for DIP and TP. Forty-three per cent of Bay over many years. annual medians fell below the reference trigger value for both DIP and TP. Corio Bay: Overall median concentrations of DIP and TP for the period were 90mg L-1 and 106µg L-1 Hobson Bay: Overall median concentrations of DIP respectively, which are second only to and TP for the period were 76 and 95µg L-1. Annual concentrations recorded at Long Reef (Table 5). median concentrations of DIP were generally Annual median concentrations of DIP and TP were between 70mg L-1 and 90mg L-1 (Figure 7). For TP generally between 80mg L-1 and 110mg L-1 (Figures 7 annual median values were generally between 80mg and 8). L-1 and 110mg L-1. Annual median concentrations were lowest in 1996 (DIP 45; TP 77µg L-1.) and highest in Concentrations of DIP and TP have increased 1990 (DIP 100; TP 123µg L-1). between 1996 and 1999 (Figures 7 and 8). There

Annual medians of DIP and TP increased between 1996 and 1999 (Figures 7 and 8).

Only 6 per cent of DIP and 0 per cent of TP annual medians fell below the reference trigger values. No values for either DIP or TP fell below the national trigger.

Long Reef: The overall median for the period DIP and TP concentrations were 121mg L-1 and 136mg L-1 respectively (Table 5). These concentrations were the highest overall median for the periods for DIP and TP in Port Phillip Bay. Annual median concentrations of IP were between 90mg L-1 and 170mg L-1 (Figure 7). Annual median concentrations of TP were between 110mg L-1 and 220mg L-1. There was considerable and consistent seasonal variability with highest DIP and TP individual values occurring between May and October.

No annual median concentration of DIP or TP was below the reference trigger values. Similarly there were no DIP or TP values below the default national trigger value.

Figure 7. Inorganic phosphate. Annual median concentrations (µg L-1) at reference and assessment sites. Error bars are the 95 per cent confidence intervals. The reference trigger value calculated from pooled reference site data is shown as a red line. The NWQMS national default trigger value is shown as a green line.

Figure 8. Total Phosphorus. Annual median concentrations (µg L-1) at reference and assessment sites. Error bars are the 95 per cent confidence intervals. The reference trigger value calculated from pooled reference site data is shown as a red line. The NWQMS national default trigger value is shown as a green line.

Silicate 350mg L-1 were usually the highest recorded in the Bay for any particular year (Figure 9). Reference Sites. At Central and Dromana sites overall median concentrations of silicate were 134mg For 81 per cent of cases the annual median silicate L-1 and 155mg L-1 respectively (Table 5). Inter-annual concentrations were greater than the reference variability, shown by the large error bars (Figure 9), trigger value. Silicate concentrations were negatively was high. The two sites closely track each other correlated (r2=0.51) with salinity and undoubtedly (Figure 9), with annual median concentrations at the reflect the influence of the discharges from the Yarra Dromana site varying from 80mg L-1 to 200mg L-1 and River.

-1 up to 280mg L at the Central site. A trigger value of Long Reef: The overall median silicate concentration -1 184mg L was set for benchmarking of other sites. No at this site was 141mg L-1 (Table 5). Annual median temporal trends in silica concentrations were values ranged between 100mg L-1 and 220mg L-1 observed. (Figure 9) but there was no evident annual or Corio Bay: The overall median silicate concentration seasonal pattern in silicate concentrations. No was 120mg L-1. Annual median silicate relationships with salinity or suspended solids were concentrations varied from 90mg L-1 to 300mg L-1. found at this site. For 20 per cent of cases annual There were no relationships between silica, salinity median silicate concentrations were greater than the and suspended solids at this site. Silicate reference trigger value. concentrations were above the reference trigger value for 31 per cent of cases.

Patterson River: The overall annual median concentration of silicate was 189mg L-1 (Table 5). The annual median silica concentrations varied from 100mg L-1 and 350mg L-1 (Figure 9). At times silicate concentrations at the Patterson River site were as high as those measured at the Hobsons Bay site. Silicate concentrations were negatively correlated (R2=0.39) with salinity and positively correlated (R2=0.23) with suspended solids. The silicate concentration at the Patterson River site was above the reference trigger value for 71 per cent of cases.

Hobsons Bay: The highest overall median silicate concentration (232mg L-1) was recorded at this site (Table 5). Similarly, annual median silicate concentrations which ranged from 100mg L-1 to

Figure 9. Silicate. Annual median concentrations (µg L-1) at reference and assessment sites. Error bars are the 95 per cent confidence intervals. The 80th percentile trigger value calculated from pooled reference site data is shown as a red line.

Chlorophyll a The median chlorophyll objective was met on 13 of the 15 years of monitoring, but was exceeded in Central: Annual median concentrations varied 1985 and 1988 (Table 4). Accounting for confidence between 0.25mg L-1 and 1mg L-1 (Figure 10) and had an intervals only on 10 of these occasions was the overall median for dataset of 0.8mg L-1 (Table 5). The objective unambiguously met (Table 6). Similarly the median chlorophyll objective was met on 14 of the 90th percentile objective was met on 12 of 15 (80 per 16 (88 per cent) years of monitoring but only on five cent) occasions, with exceedances in 1988, and of these occasions was the objective unambiguously 1993 and 1997. met (Table 7). In 1986 and 1988 the objective was exceeded unambiguously. Similarly, the 90th Patterson River: Annual median concentrations percentile objective was met on 14 of 16 occasions, varied between 0.7mg L-1 and 2.8mg L-1 (Figure 10) with exceedances in 1985 and 1993. No significant and had an overall median of 1.0mg L-1 (Table 5). trends in chlorophyll a concentrations were Chlorophyll a at this site was positively correlated detected, nor were there relationships with salinity with ammonium (R2 = 0.26), oxidised nitrogen (R2 = or suspended solids. 0.38), TN (R2 = 0.49), reactive phosphorus (R2 = 0.32), TP (R2 = 0.49) and suspended solids (R2 = Dromana: Annual median concentrations varied 0.26). It was negatively correlated (R2 = 0.35) with between 0.5mg L-1 and 1mg L-1 (Figure 10) and had an salinity suggesting phytoplankton growth following overall median of 0.6mg L-1 (Table 5). The median freshwater discharges from the Patterson River. chlorophyll objective was met on all of the seven years of monitoring. Only once did the confidence The median chlorophyll objective was met on four of intervals span the objective, but on three occasions the seven (57 per cent) years of monitoring. For the it was not possible to calculate a confidence three exceedances no confidence intervals could be interval. The 90th percentile objective was met on six calculated, while only in 1994 and 1995 did the of seven occasions, with the exceedance occurring confidence intervals fall below the objective (Table in 1995. 6, Figure 10). The 90th percentile objective was met on five of seven (71 per cent) occasions, with No significant trends in chlorophyll a concentrations exceedances in 1990, 1991 and 1993. were detected, nor were there relationships with salinity or suspended solids. Hobsons Bay: Annual median concentrations varied between 1.5mg L-1 and 4mg L-1 (Figure 10) and had an Corio Bay: Annual median concentrations varied overall median of 2mg L-1 (Table 5). No significant between 0.5mg L-1 and 1.5mg L-1 (Figure 10) and had temporal trends in chlorophyll a concentrations an overall median for the dataset of 0.9mg L-1 were detected at this site. Chlorophyll a was (Table 5). positively related (R2 = 0.18) to TN. No significant temporal trends were detected but The median chlorophyll objective was met on 12 of chlorophyll a concentrations were positively the 16 years (75 per cent) of monitoring. On only four correlated (R2 = 0.2) with total nitrogen. years was the objective unambiguously met and on

no occasions was the objective clearly exceeded. The 90th percentile objective was met on 10 of 16 occasions, with exceedances in 1989, 1990, 1991, 1993 and 1995.

Long Reef: Annual median concentrations varied between 1.2mg L-1 and 2.5mg L-1 (Figure 10) and had an overall median of 1.6mg L-1 (Table 5). The median chlorophyll objective was met on nine of 10 (90 per cent) years of monitoring, but only three of these were clear passes (Table 6). The 90th percentile objective was met on five occasions, with exceedances in 1990, 1992, 1993, 1996 and 1999. No significant temporal trends in chlorophyll a concentrations were detected at this site, though concentrations were lowest from 1996 to 1998 when rainfall was low (Figure 2). Chlorophyll a was positively related (R2=0.16) to TN.

Figure 10. Chlorophyll a. Annual median concentrations (µg L-1) at reference and assessment sites. Error bars are the 95 per cent confidence intervals. The Waters of Victoria (Schedule F6)1 environmental objective for Port Phillip Bay is shown as a green line.

Figure 11. Annual percentage of chlorophyll a (blue symbol) and Secchi depth (green symbol) meeting the Waters of Victoria (Schedule F6) objectives.

WATER CLARITY could it be concluded that the objective was unambiguously met (Table 6, Figure 12). The annual median Secchi depth at the Patterson River site met Secchi Disk Depth the Waters of Victoria (Schedule F6) objective in 43 Central: At the Central site the overall median per cent of cases. Secchi depth for the period was 6m (Table 5). The Hobsons Bay: The overall median Secchi depth for annual median Secchi depths at Central are the Hobsons Bay site was 3m (Table 5). Annual generally from 5m to 8m (Figure 12). The median median Secchi depths were generally from 2m to Secchi disk depth at the Central site was met on 15 4m. There was no temporal trends apparent in the of 16 occasions (94%) but only on 12 occasions Secchi depth data for this site. The median Secchi could it be concluded that the objective was disk depth objective was met on 14 (88 per cent) unambiguously met (Table 6). occasions in the last 16 years although on eight Dromana Bay: At the Dromana site the overall occasions there was either no confidence interval or median was 4.5m (Table 5). At the Dromana site the it spanned the objective (Table 6, Figure 12). annual median Secchi depths are generally from 4m Long Reef: The overall median Secchi depth for the to 6m (Figure 12). The median Secchi disk depth Long Reef site was 4.3m (Table 5). Annual median objective was met on two of seven occasions but in Secchi depths were between 3m and 6m (Figure 12). no instance was the confidence interval below the There was an increase in Secchi depth between 1991 objective (Table 6). and 1994. The median Secchi disk depth objective Corio Bay: The overall median Secchi depth for the was met on three of 10 occasions but only on one period at the Corio Bay site was 4.5m (Table 5). occasion did the confidence interval fall below the Annual median Secchi depths were generally objective (Table 6, Figure 12). between 3m and 6m (Figure 12). There were no trends apparent in the Secchi depth data for the Corio Bay site. The median Secchi disk depth objective was met on all 15 occasions (100 per cent) but only on 11 occasions could it be concluded that the objective was unambiguously met (Table 6, Figure 12).

Patterson River: The overall median for the period Secchi depth at the Patterson River site was 2.5m. Annual median Secchi depths at this site were generally between 2m and 4m. There were no trends apparent in the Secchi depth data for the Patterson River site. The median Secchi disk depth objective was met on all occasions but only on four of these

Figure 12. Secchi Disk Depth. Annual median Secchi depths at reference and assessment sites. Error bars are the 95 per cent confidence intervals. The Waters of Victoria (Schedule F6)1 environmental objective for Port Phillip Bay is shown as a green line.

Suspended solids between 1.1mg L-1 and 4.9mg L-1 (Figure 13). At the Long Reef site suspended solids concentrations are Reference sites: The overall median suspended below the regional trigger value in 40 per cent of solid concentrations at the Central and Dromana cases. sites were 2.7mg L-1 and 2mg L-1 respectively (Table 5). The overall median recorded for the Dromana site was the lowest recorded for Port Phillip Bay. Annual medians at the Central site were between 1.4 and 3.8mg L-1 (Figure 13). Annual medians at the Dromana site were lower and were between 0.8mg L- 1 and 3.3mg L-1.

Corio Bay: The overall median suspended solids concentration was 3.2mg L-1. Annual median suspended solids concentrations were between 1.8mg L-1 and 5.6mg L-1 (Figure 13). Suspended solids concentrations at the Corio Bay site were below the regional trigger value in 58 per cent of cases.

Patterson River: The overall median suspended solids concentration recorded at the Patterson River site was 2.5mg L-1. Annual median values were between 1.2mg L-1 and 4.3mg L-1 (Figure 13). At the Patterson River site, suspended solids concentrations were below the regional trigger value on 71 per cent of cases.

Hobsons Bay: The highest overall median suspended solid concentration was recorded at this site and this was 4mg L-1 (Table 5). Annual median suspended solid concentrations were between 3mg L-1 and 5.7mg L-1 (Figure 13). Suspended solids concentrations at the Hobsons Bay site were below the regional trigger value in 25 per cent of cases.

Long Reef: The second highest overall median suspended solids concentration was recorded at this site and this was 3.8mg L-1 (Table 5). Annual median suspended solids concentrations were

Figure 13 Suspended solids. Annual median suspended solids (mg L-1) at reference and assessment sites. Error bars are 95 per cent confidence intervals. The value of the reference trigger calculated from pooled reference site data is indicated by the red line. There are no NWQMS guidelines or SEPP values for suspended solids.

DISCUSSION emerge for the Bay and are discussed in relation to the processes causing these patterns.

Has there been a long-term improvement in the Over the 16-year dataset, the range of water column water quality in the Bay? concentrations measured is dominated by pronounced year-to-year (inter-annual) variability. One of the aims of this report was to determine if This interannual variability was largely the result of there was any long-term trends in nutrient status changes in the amount and timing of rainfall which and water clarity in Port Phillip Bay. are in turn controlled by large-scale climate One of the difficulties of any long-term monitoring is phenomena such as the El Nino Southern Oscillation to distinguish if changes in observed water column (ENSO) events which may persist for one or more concentrations of nutrients and sediment can be years. For many indicators, some of this variability attributed to human activities, or if changes are a results from seasonal patterns of input and consequence of climate variation. Another difficulty recycling. Few trends were detected over the entire is establishing the spatial extent over which dataset (Table 6) and few trends applied Bay-wide. temporal patterns in nutrient concentrations can be Trends that did occur were mainly at sites in the inferred. The distribution of nutrients, and central and eastern parts of the Bay. chlorophyll biomass in the Bay is patchy and varies Over the 16-year dataset three time periods can be in response to inputs, mixing of water masses and distinguished. Key findings from this study are remineralisation processes. Major inputs such as discussed in the context of patterns of climate the Yarra and WTP have an extensive influence on variation and human activities that may have nutrient and chlorophyll concentrations. In winter contributed to variation in nutrient and sediment the Yarra plume can be observed as a thin (< 5km loads to the Bay. wide) strip down the eastern coast as far as Dromana, but in summer this plume is usually 1984 to 1989: Data from the three sites monitored restricted to within 15km of Hobsons Bay. Similarly, during this period indicate there were relatively few plumes from WTP have been observed in winter at changes in nutrient concentrations, and no the Central site and in Corio Bay. Rather than simple significant trends were detected. Measurements of radial dilution of nutrient from these sources, nitrogen forms do not cover the entire period observations suggest that wind speed and direction because of changes in analytical techniques that are the main influence on nutrient patch integrity preclude meaningful comparison. Only ammonia and distribution.6 data from 1986 could be used. Climatic conditions, as indicated by annual rainfall (Figure 2), appear to Against this background, the single monthly be relatively stable during this period. ` samples taken at six sites in the Bay are assumed to be representative of major zones in the Bay. The 1990 to 1995: Monitoring of an additional three sites following broad spatial and long-term patterns (Patterson River, Dromana and Long Reef) commenced in this period. Significant downward

trends in nitrogen and phosphorus concentrations following diversion in 1994 of the Dandenong were found at sites mainly on the central to eastern Sewage Treatment Plant (STP). side of the Bay (Table 5). Oxidised nitrogen 1996 to 1999: Monitoring at Patterson River and concentrations tended downward at Central, Dromana sites was discontinued in 1996 for Dromana, and Corio Bay sites while at Patterson logistical reasons. During this period, phosphorus River this nitrogen trend was expressed as a concentrations at Central and Corio Bay sites reduction in ammonium concentrations. Phosphorus increased significantly, whereas the downward trend (both DIP and TP) trended downward at Central, in oxidised nitrogen continued at the Central site Dromana and Patterson River sites. The reductions since 1989 (Table 5). Neither chlorophyll, nor Secchi in nutrient concentrations at these sites were not disk depth showed any significant trends in expressed in chlorophyll concentrations. Water concentration (Figures 10 and 12) or compliance with clarity improved at Central and Long Reef sites in SEPP objectives (Figure 11). this period (Figure 12). Compliance with chlorophyll There are no compiled records on nutrient and and Secchi disk depth objectives was also greatest sediment loads for this period. Rainfall patterns during this period (Figure 11). No trends in nutrient demonstrate that the years 1996 to 1999 have been status or water clarity were observed at Hobsons Bay drier than usual (Figure 2). or Long Reef sites. Overall: Given the proximity of many of the fixed Data from the Port Phillip Bay Environmental Study2 sites to putative nutrient sources, and the sampling (PPBES) conducted during this period corroborates limitations of the present monitoring program (see these trends and provides insight into the causes Box 10) it is not unexpected there is no consistent underlying patterns in nutrient and chlorophyll trends over the whole Bay. The dominant temporal concentrations. Comprehensive fortnightly sampling feature of these records is year to year variation, of six sites and intensive underway analysis during consistent with natural climate variation rather than this period6 found similar trends. Inorganic nutrient anthropogenic influences. Thus within the range of concentrations decreased on the eastern side of the climate conditions experienced over the last 16 Bay, and water clarity improved Bay-wide, but was years it would appear that nutrient status and water most apparent on the eastern side of the Bay. clarity have been maintained. Chlorophyll a concentrations declined or stayed unchanged. This period was characterised by The findings reported here corroborate the findings increasing freshwater inputs to the Bay (Figure 2) and conclusions reached by the Port Phillip Bay resulting in an almost Bay-wide decline in salinity Environmental Study2 (PPBES) that reported from spring 1992 until early 1994, followed by a comprehensively on water quality conditions in the steady increase in salinity throughout the remainder Bay from 1990 until 1995. Drawing together previous of 1994 and 1995.6 These trends may also be related studies, the PPBES report concluded at the time that to an approximate 30 per cent reduction in N and P the Bay was in good “health”, and indicated that the loads from the Patterson/ Mordialloc main drain nutrient status of the Bay had been maintained

since routine monitoring commenced in the early result of seasonal processes as well as longer-term 1980s. Some earlier data in the PPBES report climate variation. indicates that it was probable that nitrogen levels At no site were any of the environmental objectives had decreased since the early 1970s. met in all years. In general, compliance with SEPP In the subsequent four years until 1999, the results objectives was met on greater than 75 per cent of in this report support and extend the conclusion that occasions when the annual median or percentile nutrient status and water clarity have continued to objective was accepted without regard to the be maintained since 1984. confidence intervals (Table 7). When the confidence intervals were considered the number of cases In 1996 the PPBES study also suggested that efforts where the objective was unambiguously met was were needed locally in the northern end of the Bay reduced, sometimes to no more than 30 per cent. It to reduce nitrogen loads to the Bay by could not be established whether some sites had a approximately 1000 tonnes per annum. It was greater number of exceedances. Even at Hobsons recommended these reductions could be achieved Bay and Long Reef, compliance with chlorophyll by reducing inputs from the Yarra and the urbanised objectives has generally been similar to other sites. parts on the eastern side of the Bay, and improving denitrification efficiencies of the WTP.2 To date, a The two chlorophyll objectives provide seemingly nitrogen baseline has been defined and modelling different assessments of compliance. In the period has been undertaken to identify where reductions 1984 to 1990 the median chlorophyll objective was are most achievable. With implementation of these exceeded in 1988 at all three sites, then currently actions, together with the stormwater plans monitored. However the 90th percentile objective developed by Bayside councils, it is expected that was not exceeded. In the period 1990 to 1995 nitrogen loads will reduce progressively to meet the exceedances of the 90th percentile chlorophyll 1000 tonne reduction by 2006. objective at two or more sites occurred in 1990, 1993 and 1995. But only in 1991 was the median How does water quality in the Bay compare with objective exceeded at more than two sites. Since compliance objectives? 1995 there have been no exceedances of either chlorophyll objective at more than one site in any A second aim of this report is to retrospectively one year. assess compliance with defined water quality objectives. The SEPP for the Bay establishes environmental objectives for nutrient status and water quality. Determining if these objectives were met is essential for the ongoing management of the Bay, but is often complicated by limitations of sampling and the intrinsic variation that occurs as a

CONCLUSIONS term trends were detected at either of these sites and this is likely due to the influence of these The expressed result of nutrient loads is a function nutrient sources. Although concentrations of of the geography of the Bay, the position of the nutrients were high at these two sites, compliance inputs and the wind-driven circulation. Nutrients with environmental objectives was similar to other entering the Bay will be assimilated close to shore. sites. Phytoplankton blooms will usually occur before The current design of the fixed site monitoring nutrients can be mixed offshore. Thus the main network needs refinement to provide more robust impact of nutrient load is restricted to nearshore and conclusive information to management on the waters. ecological integrity of the Bay. Improvements being Over the 16 year dataset, the range of water column considered are outlined in Box 10. concentrations measured is dominated by pronounced inter-annual variability that is due to changes in climatic conditions, which in turn affects the amount of freshwater bearing nutrients and sediment to the Bay. Few long-term trends were detected over the entire dataset or applied Bay- wide. At no site were any of the SEPP environmental objectives met in all years. Nor was there any trend in compliance to indicate a long-term change in nutrient status or water clarity.

During this time nutrient status of the Bay appears to have altered over scales of two to five years, and this has resulted principally from changing climate conditions, rather than any significant change in human activities. Within the range of climate conditions experienced over the last 16 years it would appear that the nutrient status and water clarity of the Bay have been maintained. Concentrations of the critical nutrient, nitrogen, have not increased over time and there is some evidence of a decrease.

On the western side of the Bay, Long Reef and Hobsons Bay are the two sites most heavily influenced by inputs of sediment and nutrient flowing from the WTP, and the Yarra River. No long-

Box 10. Where to from Here?

EPA is considering revision of its current monitoring program to take account of recent advances in technology and our understanding of the key ecological processes operating in the Bay. These can be summarised as:

Collection of spatially comprehensive nutrient and chlorophyll data: techniques to collect nutrient and chlorophyll data in real time are being developed which will allow greater characterization of the areas

Measuring the efficiency of sediment recycling processes: It is not possible to infer what is going on in the Bay simply by observing what happens to the concentrations of nutrients and chlorophyll in the water. Fluxes between pools of elements in the water column and in the sediment are very large and a critical factor in maintaining the health of the Bay. Denitrification has been identified as being critical to maintaining water quality in the Bay. Understanding and monitoring sediment remineralisation processes will be an essential component of ongoing monitoring.

Predictive capability for assessing algal blooms: Techniques to measure the composition and rate of primary productivity of phytoplankton will help us predict and respond appropriately to the formation of harmful algal blooms.

Meeting multiple information needs. Monitoring information is required by a number of agencies to fulfil their various reporting requirements. The monitoring being undertaken by EPA does not meet all these information needs. Discussions are being held with key agencies to develop a comprehensive monitoring network for the Bay and other major water bodies such as Gippsland Lakes and Western Port.

Linking to water quality inputs: The marine fixed site monitoring program has now been merged with the State Monitoring Network for freshwater. Greater information on loads to the Bay is essential to assessing the results from marine monitoring.

Accessibility of monitoring data: Data will soon be available through the State Monitoring Network on www.nre.gov.au. Annual summary reporting of data will be published on the internet.

Improving assessment and reporting techniques: The use of reference sites and confidence intervals will continue to be developed.

REFERENCES AND FURTHER READING Technical Report No. 24. Port Phillip Bay Environmental Study CSIRO.

References 7. Goudey R (1999). Assessing Water Quality Objectives: Discussion Paper. Environmental 1. EPA (1997). Variation of the State Water Quality Monitoring Committee. State of environmental protection policy protecting Victoria. (Waters of Victoria) - insertion of Schedule F6. Waters of Port Philip Bay. Victorian Government 8. Hogg RV, Tanis EA (1977). Probability and Gazette No. S 101 Aug 1997. Statistical Inference. Macmillan Publishing. New York. 2. Harris G, Batley G, Fox D, Hall D, Jernakoff P, Molloy R, Murray A, Newell B, Parslow J, 9. Minitab Users Guide 2 (1997). Data Analysis Skyring G, Walker S (1996). Port Phillip Bay and Quality tools. Release 12 for Windows®. Environmental Study Final Report. CSIRO. Minitab Inc. USA. Canberra, Australia. 10. Beardall J, Roberts S, Royle R (1996). 3. ANZECC (2000). Australian and New Zealand Phytoplankton in Port Phillip Bay: Spatial and Guidelines for Fresh and Marine Water Quality. seasonal trends in biomass and primary Vol. 1, The Guidelines. Prepared under the productivity. Port Phillip Bay Environmental auspices of Australian and New Zealand Study, Technical Report No. 35. Environment and Conservation Council and, 11. Nicholson GJ, Longmore AR, Cowdell RA. Agriculture and Resource Management Council (1996). Nutrient status of the sediments of Port of Australia and New Zealand. Phillip Bay. Port Phillip bay Environmental 4. Hurley P, Manins P, Lee S (2001). Year-long air Study, Technical report No. 26. pollution modelling using TAPM for the EPAV 12. Walker SJ (1999). Coupled hydrodynamic and air quality improvement plan. A report to the transport models of Port Phillip Bay, a semi Environment Protection Authority as part of enclosed bay in south-eastern Australia. Mar. their air quality improvement plan. and Freshw. Res., 50(6): 469-482. 5. Arnott GH, Gason AS, Hill DRA, Magro KL, 13. Nicholls KH (1975). A single digestion Reilly DJ Coots AG (1997). Phytoplankton procedure for rapid manual determination of composition, distribution and abundance in Kjeldahl nitrogen and total phosphorus in Port Phillip Bay from March 1990 to February natural waters. Analytica Chimica Acta. 27: 1995. Port Phillip Bay Environmental Study, 208-212. Technical Report No. 40. 14. APHA (1995) Standard methos for the 6. Longmore AR, Cowdell RA Flint R (1996). examination of water and wastewater. American Nutrient Status of the Water in Port Phillip Bay. Public Health Association (19 th ed). Washington D.C.

15. Strickland JDH, Parsons TR. (1972). A practical handbook of seawater analysis. Fisheries Research Board of Canada, Bulletin 167, Ottawa.

16. Jeffrey SW, Humphrey GF (1975). New spectrophotometeric equations for determining

chlorophylls a, b, c1 and c2 in higher plants, algae and natural phytoplankton. Biochem. Physiol. Pflanz. 167:191-198.