Baywide Water Quality Monitoring Program Milestone Report No.6

BAYWIDE WATER QUALITY MONITORING PROGRAM

MILESTONE REPORT NO.6

SEPTEMBER 2010

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

EXECUTIVE SUMMARY

Port Phillip Bay (PPB) is a large, shallow, almost landlocked bay under the influence of substantial urbanisation. Maintaining the key environmental processes of PPB is essential for sustainability. Water quality is important to a variety of assets, values and uses of PPB. There are several factors that can influence water quality in PPB, including: • Exchanges between the water column, sediment and atmosphere

• Tidal flushing from Bass Strait • Sediment, nutrient and toxicant loads in freshwater inflows, particularly from the Yarra River

• Discharges from industry and other users.

These influences are reflected in the spatial and temporal variability of water quality parameters such as toxicants, nutrients and turbidity. This is the context for the Water Quality Baywide Monitoring Program (WQBMP) associated with the Channel Deepening Project (CDP). The WQBMP has been monitoring water quality in PPB on a monthly basis since November 2007, three months prior to the commencement of dredging activities for the CDP. Generally, the results of water quality monitoring in PPB over this period are within natural variability and the expected effects of the CDP, as determined by historical range and associated statistical analyses. For the most part, water quality was within accepted guidelines. EPA identified no major areas of concern from assessment of the six month reporting period, January – June 2010. The results reported here are consistent with an understanding of water quality in PPB derived from earlier studies and other monitoring programs. Water quality in PPB continues to be influenced by rainfall and associated catchment inputs. In particular, the large rainfall event in March 2010 resulted in an inflow of nutrients, particularly nitrogen from the catchments. Phytoplankton biomass was highest along the western shores and north of the Bay refecting this distribution of available nutrients. The results from this and other programs designed to monitor the health of PPB have indicated that changes in key environmental processes and assets are within the natural variability expected for PPB. Water quality throughout PPB remains as high as it has been for at least the past 20 years and is sufficient for maintaining assets and beneficial uses.

Table of Contents Baywide water Quality monitoring Program...... 1 Milestone REport No.6...... 1 September 2010 ...... 1 Executive Summary...... 2 1. Introduction...... 9 2. Discussion ...... 12 3. Conclusions ...... 23 4. References ...... 25 Appendix 1 - Background...... 30 Appendix 2 - Methods...... 33 Appendix 3 - Results...... 44 Appendix 4 - QA/QC data and discussion...... 101 Appendix 5 - Results outside of natural/expected variability...... 104 Appendix 6. - Summary Statistics (July 2009 – June 2010)...... 108

List of Tables Table A1.1 SEPP (WoV) objectives and ANZECC trigger values...... 32

Table A2.1 Locations and corresponding SEPP (WoV) segments ...... 33 Table A2.2 EWMA control limits for listed water quality parameters...... 37 Table A2.3 Shewhart control limits for listed water quality parameters...... 38

Table A3.1 Field sampling dates and weather conditions (January – June 2010) ...... 44 Table A3.2 Summary of Exception Reports (January – June 2010) ...... 45 Table A3.3 Summary of exceedence of control limits for physico-chemical data and nutrients (January – June 2010) ...... 53 Table A3.4 Temperature Stratification in PPB (January – June 2010)...... 59

Table A5.1 PoMC/EPA Assessment (January – June 2010) ...... 105

Table A6.1 Yarra River at Newport summary statistics – Schedule F7 Yarra Port Segment Objectives...... 108 Table A6.2 Yarra River at Newport summary statistics – Schedule F6 Hobsons Segment objectives...... 109 Table A6.3 Hobsons Bay summary statistics...... 110 Table A6.4 Corio Bay summary statistics ...... 111 Table A6.5 Long Reef summary statistics...... 112 Table A6.6 Central Bay summary statistics ...... 113 Table A6.7 POM DMG summary statistics...... 114 Table A6.8 Patterson River summary statistics ...... 115 Table A6.9 Dromana summary statistics ...... 116 Table A6.10 Middle Ground Shelf summary statistics ...... 117 Table A6.11 Sorrento Bank summary statistics ...... 118 Table A6.12 Popes Eye summary statistics...... 119

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

List of Figures Figure 1 Water Quality Monitoring Program sampling sites in PPB ...... 11

Figure A2.1 DPI Nutrient cycling continuous in-situ monitoring sites ...... 40 Figure A2.2 Examples of IMOS shipborne data sampled from the Spirit of Tasmania...... 41 Figure A2.3 EPA and PoMC Beach monitoring sites ...... 42

Figure A3.1 Victorian rainfall deciles Jan – June 2010 ...... 47 Figure A3.2 Victorian rainfall deciles July – Dec 2009 ...... 47 Figure A3.3 Victorian rainfall deciles Jan - June 2009 ...... 48 Figure A3.4 Yarra River rainfall, river flow and storm events (January – June 2010) ...... 49 Figure A3.5 Patterson River rainfall and storm events (January – June 2010)...... 49 Figure A3.6 IMOS shipborne track data (March 7 - 10 2010) ...... 50 Figure A3.7 Victorian temperature deciles (January – June 2010) ...... 51 Figure A3.8 Map of WQBMP exceedences (January – June 2010)...... 52 Figure A3.9 Two Bays continuous water quality monitoring measurements (10-23 January 2010)...... 54 Figure A3.10 Surface water temperature at Central Bay (January – June 2010)...... 55 Figure A3.11 February surface water temperature across PPB and the Yarra River (2008 – 2010)...... 55 Figure A3.12 IMOS shipborne water temperature measurements for PPB (August 2008 – July 2009 and September 2009 – June 2010) ...... 56 Figure A3.13 Average salinity for PPB (January 2008 – June 2010)...... 56 Figure A3.14 Hobsons Bay surface and bottom salinity measurements (December 2009 – June 2010)...... 57 Figure A3.15 Yarra River at Newport CTD salinity profiles (January – June 2010) ...... 57 Figure A3.16 Popes Eye CTD salinity profiles (January – June 2010) ...... 58 Figure A3.17 IMOS shipborne salinity measurements for PPB (August 2008 – July 2009 and September 2009 – June 2010) ...... 58 Figure A3.18 Hobsons Bay surface salinity and chlorophyll-a measurements (December 2009 – June 2010)...... 59 Figure A3.19 Yarra River at Newport stratification (February 2010) ...... 60 Figure A3.20 CTD profile of salinity, DO and fluorescence at Yarra River Newport (March 2010)...... 60 Figure A3.21 CTD profile of salinity, DO and fluorescence at Long Reef (March 2010) ....61 Figure A3.22 Hobsons Bay surface DO measurements (January – June 2010)...... 61 Figure A3.23 CTD profile of DO and chlorophyll fluorescence at Central Bay (April 2010)62 Figure A3.24 CTD profile of DO and chlorophyll fluorescence at PoM DMG (April 2010) .62 Figure A3.25 CTD profile of salinity, temperature and DO at Central Bay (April 2010)...... 63 Figure A3.26 CTD profile of salinity, temperature and DO at PoM DMG (April 2010)...... 63 Figure A3.27 Water clarity (Secchi depth) at Yarra River at Newport (November 2007– June 2010)...... 64 Figure A3.28 Water clarity (Secchi depth) at Corio Bay (November 2007– June 2010) ....64 Figure A3.29 Yarra River at Newport CTD turbidity profile (January - June 2009; January - June 2010)...... 65 Figure A3.30 Ammonium Shewhart control chart for PoM DMG (November 2007 – June 2010)...... 66

Figure A3.31 Ammonium EWMA control chart for Dromana (November 2007 - June 2010) ...... 67 Figure A3.32 Ammonium EWMA control chart for Central Bay (November 2007 - June 2010)...... 67 Figure A3.33 Ammonium EWMA control chart for Yarra River at Newport (November 2007 - June 2010)...... 68 Figure A3.34 NOx Shewhart control chart for Central Bay (November 2007 - June 2010)68 Figure A3.35 NOx EWMA control chart for Yarra River at Newport (November 2007 - June 2010)...... 69 Figure A3.36 River flow and NOx measurements for Yarra River at Newport (May 2006 - June 2010)...... 69 Figure A3.37 Melbourne Water and EPA NOx data (January – June 2010)...... 70 Figure A3.38 NOx Shewhart control chart for Popes Eye (November 2007 - June 2010) .70 Figure A3.39 Total nitrogen Shewhart control chart for Yarra River at Newport (November 2007 - June 2010)...... 71 Figure A3.40 Total nitrogen EWMA control chart for Yarra River at Newport (November 2007 - June 2010)...... 71 Figure A3.41 Total nitrogen Shewhart control chart for Corio Bay (November 2007 - June 2010)...... 72 Figure A3.42 Total nitrogen EWMA control chart for Corio Bay (November 2007 - June 2010)...... 72 Figure A3.43 Phosphate Shewhart control chart for Corio Bay (November 2007 - June 2010)...... 73 Figure A3.44 Phosphate EWMA control chart for Corio Bay (November 2007 - June 2010) ...... 73 Figure A3.45 Phosphate Shewhart control chart for Central Bay (November 2007 - June 2010)...... 74 Figure A3.46 Phosphate EWMA control chart for Central Bay (November 2007 - June 2010)...... 74 Figure A3.47 WTP nutrient loads (January – June 2010) ...... 75 Figure A3.48 WTP phosphate loads (May 2008 – June 2010) ...... 75 Figure A3.49 Long Reef salinity and phosphate measurements (November 2007 – June 2010)...... 76 Figure A3.50 Melbourne Water and EPA phosphate water quality data (January – June 2010)...... 76 Figure A3.51 Phosphate Shewhart control chart for Dromana (November 2007 - June 2010)...... 77 Figure A3.52 Phosphate EWMA control chart for Dromana (November 2007 - June 2010) ...... 77 Figure A3.53 PPB salinity and phosphate concentrations (November 2007 - June 2010).78 Figure A3.54 Total Phosphorus Shewhart control chart for Hobsons Bay (November 2007 - June 2010)...... 78 Figure A3.55 Total Phosphorus EWMA control chart for Hobsons Bay (November 2007 - June 2010)...... 79 Figure A3.56 Total Phosphorus Shewhart control chart for PoM DMG (November 2007 - June 2010)...... 79

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.57 Total Phosphorus EWMA control chart for PoM DMG (November 2007 - June 2010)...... 80 Figure A3.58 Total Phosphorus Shewhart control chart for Dromana (November 2007 - June 2010)...... 80 Figure A3.59 Total Phosphorus EWMA control chart for Dromana (November 2007 - June 2010)...... 81 Figure A3.60 Melbourne Water and EPA total phosphorus water quality data (January – June 2010)...... 81 Figure A3.61 Silicate control chart for Yarra River at Newport (November 2007 - June 2010)...... 82 Figure A3.62 Silicate control chart for Corio Bay (November 2007 - June 2010)...... 82 Figure A3.63 Silicate control chart for Patterson River (November 2007 - June 2010)...... 83 Figure A3.64 Silicate control chart for Popes Eye (November 2007 - June 2010)...... 83 Figure A3.65 Total phytoplankton cell numbers across PPB (February 2008 – June 2010) ...... 84 Figure A3.66 Average Pseudo-nitzschia species cell counts from PPB (1998 – 1996; 2008 -2010) ...... 85 Figure A3.67 Pseudo-nitzschia species cell counts across PPB (1991) ...... 85 Figure A3.68 Pseudo-nitzschia species cell counts in PPB (1988-1996; 2008-2010)...... 86 Figure A3.69 Hobsons Bay interpolated water quality data (January – June 2010)...... 88 Figure A3.70 Corio Bay interpolated water quality data (January – June 2010) ...... 89 Figure A3.71 Yarra River at Newport and Corio Bay phytoplankton species composition (January – March 2010)...... 90 Figure A3.72 IMOS shipborne in-situ chlorophyll fluorescence measurements for PPB (August 2008 – July 2009 and September 2009 – June2010)...... 91 Figure A3.73 Chlorophyll a control chart for Yarra River at Newport (November 2007 - June 2010)...... 92 Figure A3.74 Chlorophyll a EWMA control chart for Yarra River at Newport (November 2007 - June 2010)...... 92 Figure A3.75 Chlorophyll a control chart for Corio Bay (November 2007 - June 2010) .....93 Figure A3.76 Chlorophyll a EWMA control chart for Corio Bay (November 2007 - June 2010)...... 93 Figure A3.77 Chlorophyll a EWMA control chart for Sorrento Bank (November 2007 - June 2010)...... 94 Figure A3.78 Yarra River Melbourne Water metals data (January – June 2010)...... 94 Figure A3.79 St Kilda Beach monitoring metals data (January – June 2010)...... 95 Figure A3.80 Arsenic control chart for Dromana (November 2007 - June 2010) ...... 96 Figure A3.81 Arsenic EWMA control chart for Dromana (November 2007 - June 2010) ...96 Figure A3.82 Arsenic control chart for Central Bay (November 2007 - June 2010) ...... 97 Figure A3.83 Arsenic EWMA control chart for Central Bay (November 2007 - June 2010) ...... 97 Figure A3.84 Total chromium control chart for Yarra River at Newport (November 2007 - June 2010)...... 98 Figure A3.85 Total copper Shewhart control chart for Yarra River at Newport (November 2007 - June 2010)...... 98 Figure A3.86 Dissolved copper control chart for Yarra River at Newport (November 2007 - June 2010)...... 99

Figure A3.87 Total lead Shewhart control chart for Yarra River at Newport (November 2007 - June 2010)...... 99 Figure A3.88 Dissolved lead control chart for Yarra River at Newport (November 2007 - June 2010)...... 100

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

List of Abbreviations

Australian & New Zealand Environment Conservation Council ANZECC Guidelines for Fresh and Marine Water Quality (2000) BMP Baywide Monitoring Program CDBMP Channel Deepening Baywide Monitoring Programs CDP Channel Deepening Project CTD Conductivity, Temperature and Depth profiler DIN Dissolved Inorganic Nitrogen DO Dissolved Oxygen DPI Department of Primary Industries (Victoria) EES Environment Effects Statement EPA Environment Protection Authority EWMA Exponentially Weighted Moving Average IMOS Integrated Marine Observing System LOR Limit of Reporting MU Measurement Uncertainty NATA National Association of Testing Authorities NCBMP Nutrient Cycling Baywide Monitoring Program PAR Photosynthetic Active Radiation PoM DMG Port of Melbourne Dredge Material Ground PoMC Port of Melbourne Corporation PPB Port Phillip Bay PPBES Port Phillip Bay Environmental Study PR Progress Report QA Quality Assurance QC Quality Control SEES Supplementary Environment Effects Statement SEPP (WoV) State environment protection policy (Waters of Victoria) SOP Standard Operating Procedure TBT Tributyl tin TSHD Trailing Suction Hopper Dredger VSOM Victorian Shellfish Operations Manual WQBMP Water Quality Baywide Monitoring Program WTP Western Treatment Plant

1. INTRODUCTION 1.1 Water Quality Baywide Monitoring Program

Water quality is important to a variety of assets, values and uses of Port Phillip Bay (PPB). There are several factors that influence water quality in PPB such as tidal flushing from Bass Strait, freshwater inflows, particularly from the Yarra River, and discharges from industry. Exchanges between the atmosphere, water column, aquatic plants and animals and sediment are also important. The combination of these factors affects a range of water quality parameters, including contaminants, nutrients and turbidity, which can be variable in space and time. For interpreting PPB water quality, important considerations include:

• PPB is relatively enclosed and has limited tidal exchange • PPB is under the influence of substantial urbanisation within the catchment • Growth of plants in PPB is considered to be nitrogen limited • Historically, nitrogen fixing blue-green algae have been very limited in their extent and significance in PPB • With respect to eutrophication, the ‘health’ of PPB is highly dependent upon sediment metabolic processes involving benthic infauna and areas of adjacent oxic and anoxic sediment. This favours nitrification / denitrification processes which allow nitrogen to be lost from PPB more rapidly than tidal exchange would achieve (Harris et al. 1996).

The Water Quality Baywide Monitoring Program (WQBMP) undertakes monthly monitoring of selected water quality parameters at 11 fixed sites in PPB (Figure 1) as part of the Channel Deepening Baywide Monitoring Programs (CDBMP) of the Channel Deepening project (CDP). Background to the WQBMP, including details of the EPA role in monitoring water quality in PPB, is provided in Appendix 1. Further information about the selection of all 11 sites is outlined in Appendix 2, Table A2.1. The parameters monitored and associated limits of reporting for the WQBMP are listed in section 4.1.2 and 4.1.3 of the Detailed Design Water Quality – Detailed Design CDP_ENV_MD_023 Rev 5.0 (PoMC 2010a). Algal indicators to be measured are listed in section 4.1.1 of the Algal Blooms-Detailed Design CDP_ENV_MD_012_Rev 3.0 (PoMC 2009a). The objective of the WQBMP is to: ‘Detect changes in water quality outside expected variability’.

‘Expected variability’ refers to changes in the monitored indicator/s that are expected due to ‘natural variability’ (i.e. background based on historical data) and the anticipated CDP - related changes as predicted by the Supplementary Environment Effects Statement (SEES).

1.2 Port Phillip Bay Dynamics

Port Phillip Bay (PPB) is shallow (<25 m deep) and large (2,000 km2) in relation to its catchment (about 10,000 km2). It is almost land-locked, with the narrow entrance to Bass Strait and associated sand banks (the Sands) greatly restricting exchange of water between PPB and Bass Strait. The Western Treatment Plant (WTP) supplies about half of the nutrients entering PPB, a smaller proportion of toxicants, and discharges treated water to PPB on a year-round basis, with highest flows in winter. Other nutrient and toxicant sources include rivers (principally the Yarra and Maribyrnong Rivers), streams and

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

drains, with minor inputs from the atmosphere. Most of the riverine delivery of nutrients and toxicants to PPB occurs during storms (Harris et al. 1996; Parslow et al. 1999; Sokolov and Black 1999). Storm wash-off rate depends on the intensity of the surface run-off and on the mass of transportable chemical available within the catchment that builds up between storm events. Maximum concentrations of chemicals in catchment flows occur early in the first storm after prolonged dry periods.

Nutrients and toxicants are subject to a range of physical processes once they enter PPB. These include:

• Water circulation: wind and tides drive the movement of water in PPB with tidal currents dominating on and south of the Sands; • Evaporation and stream flow: generally water loss from evaporation is nearly equal to freshwater inflows in PPB, so that except near discharges, salinity is similar to oceanic levels. Prevailing drought conditions can result in higher salinity in PPB as stream flows are reduced and evaporation is enhanced; • Residence times: the theoretical residence time for water in the centre of PPB is about one year, which is long enough for nutrients entering PPB to be taken up and recycled through the plankton many times before they could be flushed to Bass Strait. Flushing times are much shorter on and south of the Sands. The WTP discharge is predominantly wind-driven once it enters PPB, and may move toward Hobsons Bay under south and westerly winds or toward Corio Bay under north and easterly winds. The Yarra/Maribyrnong Rivers typically flow down the eastern coast of PPB. Past studies indicate that the increased plankton growth arising from these nutrient inputs might reflect these spatial patterns. Depending on the strength of the circulation, the impacts of nutrient inputs may occur some distance from the location of the input (Longmore 2006). The food supply of all animals in PPB depends on the production of plants, and associated nutrient supply. Too little nutrient may lead to restricted growth, while too much may lead to undesirable impacts from explosive growth, including aesthetic, ecosystem and human health impacts. Nitrogen has been identified as the key nutrient limiting plant growth in PPB. The Werribee and Hobsons Bay areas receive the largest nitrogen loads from land-based sources, and are thus two of the most highly productive areas of PPB as indicated by phytoplankton biomass (Longmore 2006).

Ultimately almost all of the annual nitrogen input to PPB is thought to be lost from the system as N2 gas. The process leading to this loss takes place in the sediment, and arises from the coupling of two microbial processes, called nitrification and denitrification. Maintenance of high efficiency for these processes is essential for maintaining high water quality in PPB (Harris et al.1996).

1.3 Methods and Results

Details of the water quality sampling and data assessment methods and results are presented in Appendices 2 and 3, respectively. To identify changes outside of natural variability, results are compared against derived exponentially-weighted moving-average (EWMA) and Shewhart control limits and, where applicable, to SEPP/ANZECC objectives. A discussion on quality assurance and quality control (QAQC) is provided in Appendix 4. An assessment of the results identified as outside expected variability is available as Appendix 5. Previous results for the WQBMP have been reported by EPA (EPA 2008l, m; EPA 2009m, n; 2010h).

Figure 1 Water Quality Monitoring Program sampling sites in PPB

1.4 Purpose of this Report

Milestone Report # 6 (this report) is required under the Water Quality Detailed Design (PoMC 2010a) and describes the water quality monitoring component of the Baywide Monitoring Program (BMP) for the six month reporting period from January – June 2010 inclusive, while also reflecting on the program to date (November 2007 – June 2010). Its function is to provide an overall appreciation of the status of water quality in PPB for the stated reporting period. The report summarises and interprets the information gained during the field sampling events and documented in the monthly progress reports (EPA 2008a-k; EPA 2009a-l; EPA 2010a-g) and consolidates results in the context of longer-term trends, background conditions, SEPP (WoV) objectives and control chart limits, concurrent external influences (i.e. rainfall/ river flow) and other relevant studies (including other CDBMP).

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

2. DISCUSSION

Physico-chemical Parameters Physico-chemical parameters of interest in PPB include salinity, temperature, dissolved oxygen (DO), water clarity (Secchi disc depth and turbidity), total suspended solids (TSS) and light (Photosynthetic Active Radiation (PAR)). Salinity data are useful as they may give information about the size and amount of fresh water inputs, stratification, circulation within PPB and exchange with Bass Strait. Temperature is important for control of plant growth and microbial processes, and as a contributing factor to stratification of the water column. Dissolved oxygen is essential for respiration for all living plants and animals. It also plays a key role at the sediment surface in supporting nitrification and suppressing denitrification. Water clarity and TSS are related and measured because of their impact on light availability for plants, as well as aesthetics.

Salinity, temperature, dissolved oxygen

Temperature and salinity followed expected seasonal patterns. Water temperatures across the Bay were generally warmer and extended for a longer period in late 2009 / early 2010 compared to the previous year. February 2010 temperatures were the highest recorded for the WQBMP in response to above average air temperatures. Increased catchment inputs have caused a decline in average salinity with the expected autumn peak at the lowest level for the WQBMP. Salinity within PPB is still greater than Bass Strait. DO concentrations continue to show temporal and spatial variation but remain high enough to support the ecology of PPB.

Salinity, temperature and DO are water quality parameters that are strongly inter-related. Changes in temperature and salinity can both affect the concentrations of DO. This can occur via two mechanisms: • Increased temperature and salinity directly affect the oxygen carrying capacity of water, which is reduced as temperature and salinity increase. • Temperature and salinity can affect the density of water, and under certain circumstances can lead to stratification with cooler and / or more saline water (with a consequently higher density) underlying a layer of less dense, warmer and / or fresher water. The lower layer of water is effectively isolated from the atmosphere for the period that the stratification lasts, and oxygen becomes depleted as it is consumed in respiratory processes of aquatic biota. Temperature throughout the reporting period followed expected patterns with a variation of 10 - 12 °C from summer to winter months (Figure A3.10). Air temperatures in January and February 2010 were above average for Melbourne, and sampling in both these months followed a period of consecutive days with maximum temperatures over 30°C. There is a direct relationship between mean air temperature and mean surface water temperature when averaged over a few days (Black and Mourtikas 1992). Air temperatures in summer, warmer than usual by 1.9–2.4°C, translated to warmer water temperatures recorded for the WQBMP. February surface water temperatures in 2010 were the warmest recorded since commencement of the WQBMP, with temperatures at some sites 2–4 °C hotter than in 2008 or 2009 (Figure A3.11). This was confirmed by the IMOS shipborne data which show temperatures were generally warmer across the Bay for a longer period of time in 2009/2010 compared to 2008/2009 (Figure A3.12). The continuous measurements carried out by DPI since 2002 show higher temperatures in 2007 and 2009, however the DPI instruments were out of the water for service in the period 5–16 February 2010 (Figure A3.10) and may have missed the period of peak temperature. The implications of increased temperature include: increased biological metabolic rate (by 10-30%; Mickelson 1990), lower capacity of the water to hold oxygen (by 4–6% at a

salinity of 37 psu; Parsons et al. 1984), and a likelihood of increased stratification (since surface heating is the source of the increased temperature). Temperature stratification occurred at a number of sites (Table A3.4), particularly in February 2010. The CTD profile data indicate that most of the temperature stratification events show a gradual decline in temperature with depth rather than a marked thermocline. The strongest thermal stratification occurred at the Yarra River at Newport site, where changes in temperature coincided with changes in salinity at depth, indicating colder freshwater inflows at the surface (Figure A3.19). Salinity in PPB is influenced by freshwater inflows, patterns of circulation and exchange with Bass Strait. Prior to 1997, highest salinity was usually found at the Heads (from Bass Strait), but the domination of evaporation over river flow since then has led to higher salinity in PPB than in Bass Strait. Average rainfall in the latter half of 2009 reduced average salinity in the Bay to less than 36 psu in December 2009 (Figure A3.13). Due to the continuation of average rainfall in the catchment into summer and autumn of 2010, the seasonal increase in salinity which is observed each autumn was at a lower level (<37 psu) than observed during 2008 or 2009 (Figure A3.13). Rainfall in PPB and its catchment since spring 2009 has not been sufficient to reduce salinity throughout the Bay to oceanic levels. Strong spatial variability in salinity across PPB remains. Salinity, particularly in surface waters close to significant freshwater inflows, such as Hobsons Bay near the Yarra River and to a lesser extent Patterson River and the WTP, dropped substantially following periods of rainfall (Figure A3.14). Sites closer to the Heads were generally between 35 and 36 psu, reflecting exchange with water in Bass Strait (Figure A3.16). The Corio Bay site in the Geelong Arm of the Bay, where circulation with the rest of the Bay and Bass Strait is limited and there are fewer freshwater discharges, remained above 37.5 psu throughout the summer, autumn and early winter period (Figure A3.70). The spatial variability in salinity across PPB is illustrated somewhat by the IMOS shipborne track data (Figure A3.17) and clearly by the Two Bays water quality monitoring in January 2010 (Figure A3.9). By definition (PoMC 2010), salinity stratification (greater than 10 psu difference between surface and bottom waters) did not occur during the period January to June 2010, although there was an evident halocline at the Yarra River at Newport site in both March and April 2010 following periods of high rainfall and consequent river flow (Table A3.4). In March this resulted in an unusual pattern of DO stratification at the Yarra River at Newport, with a decline of over 20% in DO from the surface to the halocline and then a subsequent increase in DO at depth in the lower saline water layer (Figure A3.20). A similar pattern for DO was observed at Long Reef in March 2010 (Figure A3.21). This unusual pattern of DO variation with depth was mimicked by the fluorescence measurements of chlorophyll at both these sites (Figure A3.20 and Figure A3.21). These indicate higher chlorophyll (and phytoplankton) at the surface that decline through the freshwater layer, with a subsequent increase in chlorophyll in the deeper saline water layers. As the samples were collected in the middle of the day, it is hypothesised that DO concentrations reflect oxygen production by phytoplankton at different abundances within the water column. A similarly interesting pattern of DO and chlorophyll fluorescence occurred in the centre of PPB during February 2010 at both the Central Bay and Port of Melbourne Dredge Material Ground (PoM DMG) sites. At these sites there was a decline in DO at depth and a corresponding increase in chlorophyll fluorescence (Figure A3.23 and Figure A3.24). This may indicate the breakdown of phytoplankton in bottom waters, consuming oxygen and releasing chlorophyll, or the net respiration of phytoplankton in deep water where light is limiting. Stratification hinders the transfer of oxygen from the upper layers to the sediment, where most oxygen consumption occurs. Although declines in DO were observed in the bottom 3m at PoM DMG and bottom 2m

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

at Central Bay in April 2010, coincident with colder temperatures and higher salinity (Figure A3.25 and Figure A3.26), the DO concentrations were still high enough (>85%) to be of no ecological concern. Similar observations were made in the centre of PPB 25 years ago (Mickelson 1990). As PPB is relatively shallow and open, stratification events are usually short and quickly broken down by wind mixing of the water column. Unless stratification increases (e.g. by increased river flow, further temperature increases or a decline in winds), and/or the supply of organic matter to the sediment increases (from increased primary production), there is the expectation that DO will remain at levels sufficient to support the ecology of PPB.

Water clarity, total suspended solids and light attenuation

Water clarity across PPB was generally good. SEPP (WoV) objectives for Secchi disc depth and light attenuation were not met at the Yarra River at Newport, which remains the most turbid of all sites due to the influence of the Yarra River. Turbidity levels were considerably lower than recorded in 2009 with no evident impact from the maintenance dredging. Light attenuation during the current reporting period was high at this site due to phytoplankton activity and the influence of the Yarra River.

Water clarity may affect light availability for primary productivity and is also important for aesthetic purposes. In addition, the amount of suspended particulate matter in the water column (as indicated by total suspended solid concentrations) can influence the health of aquatic fauna by physical action on gills (Jenkins and McKinnon 2006). Turbidity, light, Secchi depth and total suspended solids are all measures that are related to water clarity. However, the relationship between each measure is not necessarily direct or linear (Davies-Colley and Smith 2001). For example, while an increase in suspended solids will result in an increase in light attenuation and decrease in Secchi depth, properties of the particles in the water such as shape, size, and reflective nature of the surfaces will influence the degree to which light is attenuated (Davies-Colley and Smith 2001). Therefore, it is pertinent to consider at least one direct measure of water clarity and also suspended sediments due to their different biological effects. Water clarity, as indicated by Secchi disc depth was, for the most part, within historical measures and SEPP (WoV) water quality objectives. The Yarra River at Newport site is generally the most turbid area due to the large amounts of sediment transported from urban and rural catchments in the Yarra River. The central sites of PPB show little variability and are generally clear, while the water clarity at other sites is often influenced by natural and site specific processes including wind, storms, local currents and tides and phytoplankton growth. Despite maintenance dredging in the Yarra River and Hobsons Bay from November 2009 to June 2010, turbidity levels remained low (Figure A3.29) and the SEPP (WoV) Secchi depth objectives were met in May and June 2010 (Figure A3.27). Previous investigations of maintenance dredging activities have indicated that increased turbidity was not detected more than 200 metres from the active dredge, and persisted for a period of less than two hours after dredging ceased (Hale 2006a). Despite turbidity and suspended solids remaining within SEPP (WoV) objectives, the annual 90th percentile objective for light attenuation was exceeded for the Yarra River at Newport and Sorrento Bank sites (Appendix 6). At Sorrento Bank the exceedence of the SEPP (WoV) light attenuation objective was by a very small margin (Table A6.11). This may be due to tidal or wave-driven resuspension of sediments, but might also reflect the difficulty of measuring light attenuation (an integrated measure calculated over depth) at a shallow site. At the Yarra River at Newport site, the exceedence of the guideline was substantial (Table A6.2). An examination of the raw data indicates that light attenuation was very high on two occasions, in

July 2009 and February 2010. The first of these occurred during CDP dredging, when turbidity levels were high, while the second occurred during a phytoplankton “bloom”. Light attenuation at this site was above the 90th percentile objective for nine of the last 12 sampling occasions. This perhaps reflects the position of the site (in a river rather than PPB), and the freshwater influences of the site, which make it difficult for PPB SEPP (WoV) objectives to be met for some parameters.

Nutrients

Nutrients in aquatic ecosystems are significant for the role they play in primary production. Deciphering patterns and trends in nutrients in aquatic systems is difficult as they cycle through various forms within the water column and sediments. Aquatic plants and phytoplankton take up nutrients in dissolved inorganic forms (e.g. NOx, ammonium, phosphate) and dissolved organic forms (e.g. urea). Measures of total nitrogen and phosphorus include inorganic particulate forms as well as nutrients within the cells of phytoplankton and zooplankton. In the sediment, particulate forms of nitrogen and phosphorus can be remineralised into dissolved forms by micro-organisms. The processes of deamination, nitrification and denitrification can result in the release of ammonium into the water column or nitrogen gas lost to the atmosphere. Sediment nutrient cycling is strongly influenced by the oxygen regime at the sediment water interface (Murray and Parslow 1997). Plant growth in PPB is nitrogen-limited (Harris et al. 1996) and there is a hierarchy of interest in considering the various nitrogen forms. Of particular interest are the dissolved inorganic nitrogen forms, ammonium, nitrite and nitrate (NOx), because they are the most readily taken up by plants. Silicate is also of interest because historically, under certain conditions (off the Werribee coast), it may limit growth of the most abundant plankton type (diatoms) (Longmore et al. 1996). Phosphate, although in a form readily taken up by plants, is of lower interest because it is present in excess in PPB compared to inorganic nitrogen. The organic and particulate forms of nitrogen and phosphorus are also of lesser interest, as they are generally not readily available for uptake by plants. Other important factors that influence nutrient concentrations in the Bay include freshwater inflows (rivers and WTP), which discharge nutrients into the Bay; seasonal cycles in underwater light climate, which influence rates of primary productivity; and exchange rates with Bass Strait (Harris et al. 1996).

Set against this complex backdrop is the monthly instantaneous sampling of nutrient concentrations from 11 sites around PPB. The difficulty in assessing the significance of nutrient concentrations in the Bay is recognised in the SEPP (WoV) Schedule F6, which does not have objectives for nutrient concentrations. The effects of increased nutrients are assessed through their primary production response (increased phytoplankton production), with SEPP (WoV) objectives for chlorophyll-a concentrations. Assessment of nutrient concentrations for the WQBMP is via EWMA and Shewhart control limits.

Nitrogenous compounds

Total nitrogen and NOx concentrations are highest at sites close to freshwater inputs. Continued exceedences during the reporting period have occurred at the Yarra River at Newport site due to increased inflows from the catchment compared to the historical period. Winter increases in NOx, associated with Bass Strait waters, were again observed in southern PPB. A small increase in ammonium concentrations coincident with small increases in chlorophyll-a was observed across the Bay, suggesting increased grazing by zooplankton.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Total nitrogen is the sum of dissolved inorganic nitrogen, organic nitrogen and particulate nitrogen. The latter two groups include a wide range of compounds from terrestrial and aquatic plant production, such as phytoplankton cells. They are present throughout PPB in much higher concentrations than the dissolved inorganic (readily available) forms, but are thought to be resistant to decomposition to forms readily available for plant growth. In general, nutrient concentrations during the reporting period followed expected patterns with higher concentrations recorded in the north of the Bay and at sites adjacent to known nutrient sources (e.g. Long Reef near the WTP, and Yarra River at Newport and Hobsons Bay under the influence of the Yarra River). In particular, the large rainfall event in March 2010 resulted in an inflow of nutrients, particularly nitrogen, from the catchments. This is illustrated in the Melbourne Water data collected from the Yarra River, which saw peaks of total nitrogen (4745 µg/L) and NOx (920 µg/L) in the Yarra River (Figure A3.37). This was also reflected in high NOx and total nitrogen concentrations at the Yarra River at Newport site (Figure A3.36 and Figure A3.39). During the past year, control limits for NOx and total nitrogen have continually been exceeded at the Yarra River at Newport site. These exceedences are a response to the increased rainfall and associated catchment flows since late 2009. The control limits for this site were calculated from 12 data points collected during prevailing drought conditions in 2006/2007 when catchment flows rarely exceeded 1500ML/day and NOx concentrations were typically <50µg/L. With a resumption of normal rainfall patterns, flows from late 2009 have been considerably greater than for the background period, reaching as high as 5000ML/day in March 2010 with NOx concentrations consistently exceeding 100µg/L (Figure A3.36). The same pattern is also evident for total nitrogen. The most southern sites (Sorrento Bank and Popes Eye, and to a lesser extent Middle Ground Shelf (MGS) and Dromana) saw increases in NOx concentrations during April-June 2010. This is consistent with the intrusion of Bass Strait water as a source of NOx to southern PPB in winter (Figure A3.38; EPA 2010h). A trend of increasing ammonium concentration between January and April–May 2010 was observed in both the raw data and EWMA transformed data at most sites, excluding Hobsons Bay, Corio Bay and Long Reef. The increase was greatest at the Yarra River at Newport and smallest at Popes Eye and Sorrento (about 50, 2 and 2 µg/L respectively), with the increase at the Yarra River at Newport due mostly to the March 2010 high flow event (Figure A3.33). The Baywide increase is unlikely to have been caused by increased Yarra discharge because no such change was observed at Hobsons Bay. Increasing discharge of ammonium from the WTP in May–June 2010 (Figure A3.47) was matched by an increase at Long Reef in June, but WTP is unlikely to have caused the increasing trend in ammonium concentrations in the rest of PPB because it began before the WTP discharge increased. This pattern of increasing ammonium concentrations can be indicative of nutrient cycling within the Bay. Data from the Nutrient Cycling Baywide Monitoring Program (NCBMP) indicates that changes to benthic nutrient recycling rates are unlikely to be the cause of the observed increases in ammonium concentration, as benthic inorganic nitrogen (ammonium plus NOx) fluxes declined by 66% at Hobsons Bay and by 19% at Central PPB between February and May 2010 (Longmore and Nicholson 2010a, b). The most likely cause of increased ammonium concentrations is zooplankton grazing. When zooplankton consume phytoplankton, nitrogen is released to the water column, either by leakage of cell contents when cells are ruptured or by excretion as ammonium from the zooplankton. More than 60% of primary production is recycled in the water column, principally by grazing (Murray and Parslow 1999). An increase in ammonium concentration coincident with an increase in chlorophyll-a concentration (0.5–1.0 µg/L between January and June 2010 at most sites) is consistent with these processes.

Denitrification (the process which removes most of the nitrogen from PPB) increases with increasing water residence time (Seitzinger et al. 2006). Under drought conditions, residence time of water in PPB would be expected to increase, along with rates of denitrification. With a return to normal rainfall patterns in the past six months, residence time in PPB would be expected to decrease as rainfall on the Bay and freshwater flows from the catchment increased. The relatively small changes in salinity observed during the reporting period suggest residence time did not change greatly, and denitrification efficiency during this reporting period (in February and May 2010; Longmore and Nicholson 2010a, b) was not significantly different to that estimated in 2008 or 2009. Ammonium concentrations at Dromana continued to exceed EWMA control limits (Figure A3.31). The control limit set for this site was based on limited data (30 records from 1994-2006) and is low compared to other sites in the Bay. In comparison, the ammonium EWMA control limit for the Central Bay site (based on over 100 records from 1994 to 2007) is 9.9µg/L, nearly double that of Dromana. The ammonium concentrations in the centre of PPB are theoretically expected to be lower than those that are inshore, which are subject to more direct influences of nutrient rich, freshwater inflows from rivers and storm water drains (Murray and Parslow 1997; PoMC 2008).

Phosphorous compounds and silicate

WTP continues to be the principal source of phosphate into PPB. The decline in concentration seen during 2008-2009 and partial recovery in 2010 is almost certainly due to changes in the discharge from WTP. The key process affecting phosphate concentrations over most of PPB remains dilution. Silicate concentrations were again highest at the Yarra River and lowest in the south of the Bay. There is some evidence to suggest recycling of silicate from the sediment is a key source for phytoplankton growth independent of external inputs.

The WTP is the principal source of phosphorus to the bay (800-1,500 t y-1 between 1996 and 2008; Melbourne Water WTP monitoring data), with the Yarra River and other streams of secondary importance (200-600 t y-1; Harris et al. 1996). About as much phosphorus (1,000-1,900 t; Harris et al. 1996) is held in PPB waters as enters each year from the catchment. Because phosphate is far in excess of that needed for plankton growth, its distribution is governed by dilution, and the primary loss is via flushing to Bass Strait. The historical spatial distribution for phosphate shows concentrations decreasing in the following order: Long Reef, Corio Bay, Yarra River at Newport and Hobsons Bay, Central Bay and near shore PPB, and south of the Sands. Over the past two years (since May 2008), there has been a substantial (30-50%) downward trend in phosphate concentration at most sites in PPB, with a partial recovery at some sites since January 2010 (Figure A3.48). Assuming that WTP remains the most significant source of phosphate to PPB, the decline could indicate either: • A decline and subsequent partial increase in the input (from WTP) or

• An increase and decrease in dilution (exchange with Bass Strait) As soils dry, the bonds attaching phosphate to soil particles weaken (Kerr et al. 2010). When soils are subsequently wetted, phosphate is released to the runoff. Phosphate concentrations are therefore high in high flows following dry periods (Sokolov and Black 1999) and the Yarra River may have contributed significant amounts of phosphate to the Bay during the high-flow events in spring 2009. However, it is clear from the Melbourne water data (Figure A3.50) that there was no correlation between river flow and

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

phosphate concentration in the Yarra River during January to June 2010, and the increase in phosphate concentration at the Yarra River at Newport over the same period reflected increases in the rest of the Bay. This confirms that even in the mouth of the Yarra, the main source of phosphate is the WTP, and not the Yarra River catchment. Alternative terrestrial sources of phosphate are therefore discounted as a reason for increased phosphate concentrations over the reporting period. Mixing diagrams (Boyle et al. 1974; Cifuentes et al. 1990; Longmore et al. 1999) may be used to infer the number of sources of nutrients to a water body, and also whether any process other than dilution (e.g. algal uptake, loss to sediment) is occurring. Mixing diagrams are based on the premise that if a nutrient is neither consumed nor regenerated during its residence in a bay or estuary, its concentration should vary linearly with salinity. This is because the only important process occurring is dilution of the discharge with bay water, and ultimately with the open ocean. Conversely, non-linear variations may indicate the importance of other processes, such as uptake by plants. Mixing diagrams are used here to indicate if there has been a change in the key process (dilution) that has been assigned to phosphate in both major studies of PPB (MMBW/FWD 1973; Harris et al. 1996).

When applied to samples from Long Reef (the site closest to WTP) collected since November 2007, data below a salinity of about 37.5 psu fits to a straight line on a plot of phosphate concentration versus salinity (Figure 3.52). The data indicates linear mixing of WTP water at an initial phosphate concentration of 7,000 µg/L with Central PPB water. In this case, phosphate concentration decreases as salinity increases, as the nutrient-rich freshwater mixes with Bay water. When applied to all the southern sites (Figure 3.53) two straight lines are apparent. The first applies to all of the sites south of and including Central PPB, and in this case phosphate concentration decreases as salinity decreases. This implies the key process is dilution of PPB water with less saline (and phosphate-poor) Bass Strait water. The second straight line applies to samples from Corio Bay. Phosphate again decreases as salinity decreases but at a lower slope than the other sites, indicating evaporation is an important process in Corio Bay. The lower slope indicates there is also another process, presumably algal uptake, that accounts for a small proportion of phosphate in Corio Bay. Mixing diagrams for sites to the north of Central PPB indicate that WTP is still the only significant phosphate source in PPB. Throughout the monitoring period, benthic flux measurements (Longmore and Nicholson 2010b) have indicated that about 55–70% of the phosphate from recycling of organic matter is trapped in the sediment, and there has been no change between May 2008 and May 2010 to indicate increased burial in the sediment. There is no evidence from this analysis that the processes affecting phosphate concentration have changed during the WQBMP, despite apparent trends, both up and down, in concentration. The phosphate load discharged from the WTP declined from July to December 2008, increased from February to June 2009, declined from June to December 2009 and increased from January to June 2010 (Figure A3.48). These changes match the observations in PPB, with the increase in load in February to June 2010 shown as a “flattening” of the downward trend in the observations in PPB. This most likely reflects the time it takes for the WTP discharge to mix into the deeper central water mass. In summary, there is no evidence during the WQBMP of a change in the number of phosphate sources to the Bay or the amount buried in the sediments, and the key process affecting phosphate concentration over most of PPB remains dilution. The decline in Baywide phosphate concentrations through 2008-09 and subsequent recovery in 2010 was almost certainly caused by changes to the discharge from the WTP. Nitrogen remains the limiting nutrient for plant growth, and the phosphate decline and subsequent increase at some sites has no consequence for the health of PPB.

Silicate concentrations varied throughout the Bay, with highest concentrations (up to 900 µg/L) at the Yarra River at Newport following the high-flow event in March 2010 (Figure A3.61), and lowest concentrations at the sites nearest Bass Strait (about 40 µg/L at Sorrento Bank and Popes Eye (Figure A3.64)). The available evidence indicates that the main catchment source of silicate to PPB during the reporting period was the Yarra River. This is consistent with earlier measurements (Sokolov 1996; Harris et al. 1996; Longmore et al. 1996). The Yarra River silicate load estimate of 3,900 t y-1 in 1995 was based on higher river flows than has occurred since the WQBMP began, and the estimated annual load from the WTP (about 800t in 1995) may form a more significant proportion of the total load now than it did during the Port Phillip Bay Environmental Study (PPBES). Benthic flux measurements (DPI unpublished data) suggest that recycling of silicate from the sediment in 2002-10 could have supplied about 12,000 t y-1; well in excess of known terrestrial inputs. Recycling from the sediment may be a key source of silicate for plankton growth throughout the Bay, independent of external inputs. Comparisons of inorganic nitrogen, phosphate and silicate concentrations indicated that at all sites the inorganic nitrogen to phosphate ratio was about one-tenth of that needed for plankton growth, indicating nitrogen is still the growth limiting nutrient. The inorganic nitrogen to silicate ratio also indicated strong nitrogen limitation at all sites, except at Long Reef in March and Popes Eye in June 2010. In both these cases, nitrogen and silicate concentrations were nearly in balance with demand.

Phytoplankton and chlorophyll-a

While phytoplankton populations were considerably lower than blooms recorded during late 2009, potentially harmful phytoplankton species (diatoms and dinoflagellates) were detected in substantial numbers. Pseudo- nitzschia species, Alexandrium catenella and Karlodinium species were all detected above Victorian Shellfish Operations Manual (VSOM) warning levels for the first time during the WQBMP. The SEPP (WoV) annual objectives for chlorophyll-a were not met at the Corio Bay, Yarra River at Newport and Patterson River sites due to the peaks in phytoplankton biomass over the past year.

Phytoplankton is the most significant primary producer in PPB, accounting for the majority of net primary production (Beardall and Light 1997). Despite this, biomass is generally low compared to similar estuaries and bays within Australia and internationally (Harris et al. 1996). It was suggested by Beattie et al. (1997) that the phytoplankton biomass within PPB is maintained at these low levels by zooplankton grazing, thereby providing a rapid flow of the products of photosynthesis into the food chain. Although low, phytoplankton biomass within PPB is highly variable across space and time. Available nutrients, light and temperature are considered the most important factors influencing phytoplankton growth in PPB (Wood and Beardall 1992). Greater biomass generally occurs within Hobsons Bay and the Yarra River, and lower biomass is generally recorded in the south of PPB reflecting the distribution of available nutrients. Temporal trends in phytoplankton biomass are more difficult to characterise, but biomass is generally higher during summer / autumn months than over winter, reflecting seasonal patterns of light and temperature (Beardall et al. 1997). The pattern of phytoplankton biomass (as reflected by chlorophyll-a concentrations) over the period January to June 2010, was consistent with these historical trends of spatial and temporal variability. The IMOS shipborne data shows both spatial and temporal variability in chlorophyll fluorescence (Figure A3.72). Along the route followed by the ship from Hobsons Bay, through central PPB to Bass Strait, chlorophyll fluorescence was always highest in Hobsons Bay and lowest at the Heads. Chlorophyll fluorescence measurements from the Two Bays monitoring program in January 2010 also provide a spatial snapshot of

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

coastal plankton patterns in the Bay (Figure A3.9). Highest chlorophyll concentrations were seen along the western shores and north of the Bay associated with nutrients from nearby sources (Figure A3.9). SEPP (WoV) water quality objectives for chlorophyll-a are based on annual medians and 90th percentiles to integrate seasonal variability. Annual medians and 90th percentiles for chlorophyll-a calculated over the period July 2009 to June 2010 were within SEPP (WoV) objectives at most sites. The exceptions were exceedences of the 90th percentile objectives at the Yarra River at Newport, Corio Bay and Patterson River (Appendix 6). EWMA control limits were also exceeded at the Yarra River (Figure A3.74) and Corio Bay sites (Figure A3.76), driven by peaks in phytoplankton biomass in February 2010 at both sites and May 2010 in Corio Bay (Figure A3.73and Figure A3.75). High cell counts from both the Yarra River at Newport and Corio Bay sites once again did not correspond with the chlorophyll-a data. There are a number of possible explanations for the inconsistency in cell counts and chlorophyll-a concentrations. Different species of phytoplankton can contain different amounts of chlorophyll-a depending on their size, dominant pigments and responses to environmental variables such as light and temperature. During this reporting period, there were significant shifts in phytoplankton community composition that may account for the disparity between cell counts and chlorophyll-a concentrations.

The phytoplankton community at the Yarra River at Newport site, although dominated by diatoms, had a shift in species composition from January to February and again in March 2010. In January a potentially harmful species from the Pseudo-nitzschia delicatissma group and Skeletonema costatum were the most dominant species. In February, the diatom S. costatum was dominant, while in March, when cells numbers plummeted but chlorophyll-a concentrations did not, there was a mixture of species present but no clear dominant species (Figure A3.71). There was also a shift in dominant species at Corio Bay over this time period. In January 2010, Skeletonema japonicum/pseudocostatum was the dominant species. In February, when cell counts decreased, but chlorophyll-a increased, cryptopytes and dinoflagellates where the most numerous phytoplankton groups. In March, where cell numbers increased, but chlorophyll-a concentrations decreased, diatoms were once again the dominant group in the phytoplankton community (Figure A3.71). Peaks in phytoplankton populations (total cells) observed during this reporting period were considerably lower than blooms recorded earlier in the WQBMP, such as those seen at the Yarra River at Newport and Hobsons Bay in November and December 2009 and in Corio Bay in April 2009 (Figure A3.65). The presence of potentially harmful species (Pseudo-nitzschia species, Alexandrium catanella and Karlodinuium species) in substantial numbers, have not previously been recorded during the WQBMP. Notification was provided to the Department of Sustainability and Environment (DSE) on each occasion that identified potentially harmful species detected above VSOM warning levels. The P. delicatissma group contains two species that are difficult to distinguish (P. delicatissma and P. pseudodelicatissma), and for the purposes of the WQBMP are counted together. Although this group of species has the potential to produce domoic acid which causes amnesic shellfish poisoning, they are not known to produce the toxin in Australia (Hallegraeff 1994). Adopting a precautionary approach, the Victorian Marine Biotoxin Management Plan (VMBMP) sets a threshold for warnings to shellfish farmers in PPB at 100,000 cells/ L and suspension of shellfish harvesting at 500,000 cells / L (Walker 2009). Numbers of P.delicatissma group above the warning and suspension thresholds were recorded in the Yarra River at Newport (987,000 cells/L) and Hobsons Bay (3,650,000 cells/L) in January 2010 (Figure A3.68) and in Corio Bay (535,000 cells/L) in April 2010. These sites are remote from existing shellfish farming areas in PPB and no closures to shellfish harvesting occurred in PPB due to these threshold exceedences during the period April 2009-April 2010 (A. Clarke, DPI, pers. comm.).

The 2010 Pseudo-nitzschia blooms were short lived, localised and followed a peak and decline of other diatom species. The January Pseudo-nitzschia bloom in the north of the Bay followed a peak and decline of S. japonicum/pseudocostatum in December 2009, while the April Pseudo-nitzschia bloom in Corio Bay followed a peak and decline of Cylindrotheca closterium in Corio Bay in March 2010. The growth of P. delicatissma group is reportedly linked to NOx concentrations and potentially nitrate to silicate ratios (Parsons and Dortch 2002). It is possible that following the decline in blooms of other diatoms, nitrate and silicate were released into the water column making conditions suitable for growth of Pseudo-nitzschia. In the Yarra River, the decline of S. japonicum/pseudocostatum occurred following heavy rains in late December/early January. This is consistent with reports of the ecology of Skeletonema spp. from elsewhere, where decreases in salinity following heavy rain led to a decline in the species and subsequent rise of an opportunistic species (Han et al. 2002).

These species have a relatively constant low level presence in PPB, and previously blooms of this species in PPB and other southern Australian waters were considered common (Hallegraeff 1994). The species bloomed in PPB in 1991/1992 with a peak of 4,200,000 cells/L in December 1991, and again in September 1996 with a peak of 2,800,000 cells/L (Longmore 2010; Figure A3.68). On several occasions in the past (most notably 1991), the bloom extended across many areas of the Bay including Grassy Point in the East, through Hobsons Bay to Dromana in the south (Longmore 2010; Figure A3.67). Alexandrium spp. are potentially harmful dinoflagellates that have been known to result in the presence of toxins in mussels in PPB in the past, with paralytic shellfish poisons detected in tissue samples from a number of locations in the Bay (Arnott et al. 1997). Alexandrium catenella was detected in the Yarra River at Newport in February 2010 at 4,100 cells/L. The VSOM levels for A. catenella are 200 cells/L for a warning issued to growers and 500 cells/L for suspension of harvest (Walker 2009). Alexandrium spp. are cyst forming species. Cysts were abundant in the sediments of the Yarra River and Hobsons Bay in 1994 (Arnott et al, 1994), although not detected in more recent surveys (Hale 2006b). Release of the cysts from the sediment is thought to be controlled by increasing day length, increased temperatures and nutrient concentrations (Sgrosso 2006). Past blooms in Hobsons Bay have all been preceded by heavy rainfall or storm events. It is likely that the prolonged drought over the past decade resulted in a lack of opportunities for germination of cysts in the sediments of Hobsons Bay. The return of average rainfall, increased catchment inputs and the summer storm events that resulted in a combination of warm water temperatures and increased nutrients provided suitable conditions for germination and growth. Karlodinium spp. are small unarmoured dinoflagellates usually considered together with members of the Karenia genus. Members of the group are known to cause fish deaths, but the mechanism is unknown (Walker 2009). VSOM warning levels for Karlodinium spp. start at 100,000 cells/L, however it is widely thought that Karlodinium spp. in general and Karlodinium australe in particular are not toxic (Mooney et al. 2009). The ecology of Karlodinium is not well documented, but it is thought to be inhibited by low salinity and this may be why conditions in Corio Bay were suitable for growth in March and April 2010, when salinity was greater than 38.2 psu. As previously stated, WQBMP monitoring sites where elevated levels of potentially harmful phytoplankton were detected during the reporting period are remote from existing shellfish farming areas in PPB and no closures to shellfish harvesting occurred in PPB due to exceedence of phytoplankton threshold levels during the period April 2009-April 2010 (A. Clarke, DPI, pers. comm.).

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Metals

Concentrations of heavy metals in the waters of PPB remain low. Most metals are transported to PPB through the catchment inflows following heavy rain, as evident in the Melbourne Water and Beach monitoring program data.

Heavy metals in the waters of PPB, with the exception of arsenic, are low compared to ranges found in estuaries and close to values for coastal waters (Fabris and Monahan 1995). Metals from the catchment are transported through the rivers, streams and drains that discharge into PPB, with the greatest loads received in the first few hours following heavy rain. The majority of metals occur in particulate form, and sedimentation removes a significant proportion of the incoming load from the water column (Fabris and Monahan 1995). The results from the sampling period January to June 2010 are consistent with this understanding of heavy metals in PPB. This is evident mostly in peaks in metal concentrations following heavy rain and peak river flow in March 2010 from the Melbourne Water and Beach monitoring data (Figure A3.78 and Figure A3.79). The majority of samples from the WQBMP contained very low concentrations of metals. There was only one occasion where a metal concentration exceeded the control limit i.e. chromium at the Yarra River at Newport, predominantly in particulate form. In the particulate state, metals pose a lower ecological risk as they cannot be taken up directly by organisms, and toxicity is therefore reduced (Goossens and Zwolsman 1996).

3. CONCLUSIONS

The WQBMP has been monitoring water quality in PPB on a monthly basis since November 2007, three months prior to the commencement of dredging activities for the CDP. Generally, the results of water quality monitoring in PPB over this period are within natural variability and the expected effects of the CDP, as determined by historical range and associated statistical analyses. For the most part, water quality was within accepted guidelines. A summary of results from the current reporting period January – June 2010 are presented below:

• Temperature throughout the reporting period varied by 10 - 12°C from summer to winter months, with an extended period of elevated water temperatures from late 2009 to early 2010. • February surface water temperatures were the highest recorded at most sites for the WQBMP following above average summer air temperatures. • Salinity in PPB is still higher than Bass Strait. Average salinity has declined in PPB with historical autumn peaks at their lowest level since commencement of the WQBMP. • DO concentrations continue to show temporal and spatial variation but remain high enough to be of no ecological concern. • Water clarity across PPB was generally good. The Yarra River at Newport remains the most turbid site due to the influence of the Yarra River. • SEPP (WoV) objectives for light attenuation were met at most sites. The influence of the Yarra River and increased phytoplankton activity were the causes of poor light attenuation at the Yarra River at site. • Total nitrogen and NOx concentrations were highest close to freshwater inputs. Increased catchment flows have resulted in continued exceedences at the Yarra River at Newport. • Winter increases in NOx associated with water from Bass Strait were again observed in southern PPB. • Small increases in ammonium and chlorophyll-a were observed across many areas of PPB suggesting grazing by zooplankton. • WTP continues to be the main source of phosphate into PPB with changes in concentrations reflecting changes in discharges. • Recycling of silicate from the sediments may be a key source for phytoplankton (diatoms) independent of external sources. • Potentially harmful phytoplankton species (diatoms and dinoflagellates) were detected in substantial numbers for the first time during the WQBMP, but the relevant sites were remote from shellfish farming areas in PPB and no closures to harvesting occurred. • SEPP (WoV) chlorophyll-a objectives were not met at the Yarra River at Newport, Corio Bay and Patterson River sites due to peaks in phytoplankton biomass over the past year. • Metal concentrations remained low and consistent with historical studies. EPA identified no major areas of concern from assessment of the current reporting period. The results reported here are consistent with an understanding of water quality in PPB derived from earlier studies and other monitoring programs.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

The results from this and other programs designed to monitor the health of PPB have indicated that changes in key environmental processes and assets are within the natural variability expected for PPB. Water quality throughout PPB remains as high as it has been for at least the past 20 years and is sufficient for maintaining assets and beneficial uses.

4. REFERENCES

ANZECC 2000. Australian and New Zealand Guidelines for Fresh and Marine Water Quality (2000), Australian and New Zealand Environment Conservation Council. Arnott, G., Conron, S., Reilly, D., Hill, D. and Sonneman, J., 1994, Effects of channel maintenance dredging on the mobilization and translocation of toxic algal cysts in Port Phillip Bay, Report to Port of Melbourne Authority, Victorian Fisheries Research Institute, Queenscliff, Victoria Arnott, G., Gason, A., Hill, D., Margo, K., Reilly, D. and Coots, A., 1997, Phytoplankton composition, distribution and abundance in Port Phillip Bay from March 1990 to February 1995, Port Phillip Bay Environmental Study, Technical Report No.40, CSIRO, Melbourne. Beardall, J. and Light, B., 1997, Microphytobenthos in Port Phillip Bay: Distribution and primary productivity, Port Phillip Bay Environmental Study, Technical Report No.30, CSIRO, Melbourne. Beardall J., Roberts S. and Royle, R., 1997. Phytoplankton productivity in Port Phillip Bay: seasonal and spatial distributions. Technical Report No. 35, CSIRO Port Phillip Bay Environmental Study, ACT. Black, K.P and Mourtikas, S 1992. Literature review of the physics of Port Phillip Bay, Port Phillip Bay Environmental Study Technical Report No.3 Boyle, E.A., Collier, E.R., Dengler, A.T., Edmond, J., Ng, A.C. and Stallard, R.F. 1974. On the chemical mass balance in estuaries. Geochim. Cosmochim. Acta 38, 1719-1728. Cifuentes, L.A., Schemel, L.E. and Sharp, J.H. 1990. Qualitative and numerical analyses of the effects of river inflow variations on mixing diagrams in estuaries. Estuarine, Coastal and Shelf Science 30, 411-427. Davies-Colley, R. J. and Smith D.G, 2001. Turbidity, Suspended Sediment, and Water Clarity: A Review. Journal of the American Water Resources Association 37: 1085–1101. EPA 1999 Variation of the state environment protection policy (Waters of Victoria) - insertion of schedule F7. Waters of the Yarra catchment. Victorian Government Gazette S 89. EPA 2003 Variation of the state environment protection policy (Waters of Victoria) – Schedule to the order in council. Victorian Government Gazette S 107. EPA 2008a. Baywide Water Quality Monitoring Program Progress Report No 1. (November 2007 – January 2008), March 2008, EPA. EPA 2008b. Baywide Water Quality Monitoring Program Progress Report No 2. (February 2008), April 2008, EPA. EPA 2008c. Baywide Water Quality Monitoring Program Progress Report No 3. (March 2008), May 2008, EPA. EPA 2008d. Baywide Water Quality Monitoring Program Progress Report No 4. (April 2008), May 2008, EPA. EPA 2008e. Baywide Water Quality Monitoring Program Progress Report No 5. (May 2008), June 2008, EPA. EPA 2008f. Baywide Water Quality Monitoring Program Progress Report No 6. (June 2008), July 2008, EPA. EPA 2008g. Baywide Water Quality Monitoring Program Progress Report No 7. (July 2008), August 2008, EPA.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

EPA 2008h. Baywide Water Quality Monitoring Program Progress Report No 8. (August 2008), September 2008, EPA. EPA 2008i. Baywide Water Quality Monitoring Program Progress Report No 9. (September 2008), October 2008, EPA. EPA 2008j. Baywide Water Quality Monitoring Program Progress Report No 10. (October 2008), November 2008, EPA. EPA 2008k. Baywide Water Quality Monitoring Program Progress Report No 11. (November 2008), December 2008, EPA. EPA 2008l. Baywide Water Quality Monitoring Program Milestone Report No 1. July 2008, EPA.

EPA 2008m. Baywide Water Quality Monitoring Program Milestone Report No 2. November 2008, EPA. EPA 2009a. Baywide Water Quality Monitoring Program Progress Report No 12. (December 2008), January 2009, EPA. EPA 2009b. Baywide Water Quality Monitoring Program Progress Report No 13. (January 2009), February 2009, EPA. EPA 2009c. Baywide Water Quality Monitoring Program Progress Report No 14. (February 2009), March 2009, EPA. EPA 2009d. Baywide Water Quality Monitoring Program Progress Report No 15. (March 2009), April 2009, EPA. EPA 2009e. Baywide Water Quality Monitoring Program Progress Report No 16. (April 2009), May 2009, EPA. EPA 2009f. Baywide Water Quality Monitoring Program Progress Report No 17. (May 2009), June 2009, EPA. EPA 2009g. Baywide Water Quality Monitoring Program Progress Report No 18. (June 2009), July 2009, EPA. EPA 2009h. Baywide Water Quality Monitoring Program Progress Report No 19. (July 2009), August 2009, EPA. EPA 2009i. Baywide Water Quality Monitoring Program Progress Report No 20. (August 2009), September 2009, EPA. EPA 2009j. Baywide Water Quality Monitoring Program Progress Report No 21. (September 2009), October 2009, EPA. EPA 2009k. Baywide Water Quality Monitoring Program Progress Report No 22. (October 2009), November 2009, EPA. EPA 2009l. Baywide Water Quality Monitoring Program Progress Report No 23. (November 2009), December 2009, EPA. EPA 2009m. Baywide Water Quality Monitoring Program Report No 3. May 2009, EPA.

EPA 2009n. Baywide Water Quality Monitoring Program Report No 4. October 2009, EPA.

EPA 2010a. Baywide Water Quality Monitoring Program Progress Report No 24. (December 2009), January 2010, EPA.

EPA 2010b. Baywide Water Quality Monitoring Program Progress Report No 25. (January 2010), February 2010, EPA. EPA 2010c. Baywide Water Quality Monitoring Program Progress Report No 26. (February 2010), March 2010, EPA. EPA 2010d. Baywide Water Quality Monitoring Program Progress Report No 27. (March 2010), April 2010, EPA. EPA 2010e. Baywide Water Quality Monitoring Program Progress Report No 28. (April 2010), May 2010, EPA. EPA 2010f. Baywide Water Quality Monitoring Program Progress Report No 29. (May 2010), June 2010, EPA. EPA 2010g. Baywide Water Quality Monitoring Program Progress Report No 30. (June 2010), July 2010, EPA EPA 2010h. Baywide Water Quality Monitoring Program Report No 5. March 2010, EPA. Fabris, G.J. and Monahan, C.A., 1995. Characterisation of Toxicants in Waters from Port Phillip Bay: Metals. CSIRO INRE Port Phillip Bay Environmental Study Technical Report No. 18. ISSN 1039-3218. CSIRO. Fabris, G.J., Monahan, C.A., Werner, G.F. and Theodoropoulos, T., 1995. Impact of Shipping and Dredging on Toxicants in Port Phillip Bay, Port Phillip Bay Environmental Study Technical Report No. 20, CSIRO.

Goossens, H. and Zwolsman, J., 1996, An Evaluation of the Behaviour of Pollutants During Dredging Activities, Terra et Aqua 62: 20-28.

Hale, J., 2006a, Maintenance Dredging Campaign: Water Quality Monitoring In The Dredge And Disposal Plumes, Report to PoMC, Melbourne.

Hale, J., 2006b, Appendix 1, Phytoplankton Blooms in Longmore AR (2006), Channel Deepening Project Supplementary Environmental Effects Statement Head Technical Report: Nutrient Cycling. Marine and Freshwater Systems l Report Series No.17. Primary Industries Research Victoria: Queenscliff. Hallegraeff, G.M., 1994, Species of the Diatom Genus Psuedo-nitzschia in Australian Waters. Botanica Marina, 37: 397 - 411. Han, M-S., Furuya, K. and Nemoto, T., 1992, Species specific productivity of Skeletonema costatum in the inner part of Tokyo Bay, Marine Ecology Progress Series 79: 267-273.

Harris, G., Batley, G., Fox, G., Hall, D., Jernakoff, P., Molloy, R., Murray, A., Newell, B., Parslow, J., Skyring, G. and Walker, S. 1996. Port Phillip Bay Environmental Study Final Report. CSIRO, ACT. Jenkins, G.P. and McKinnon, L., 2006, Channel Deepening Supplementary Environment Effects Statement – Aquaculture and Fisheries. Internal Report No. 77, Primary Industries Research Victoria, Queenscliff.

Kerr, J.G., Burford, M., Olley, I. and Udy, J. (2010). The effects of drying on phosphorus sorption and speciation in subtropical river sediments. Marine and freshwater research 61, 928-935. Longmore, A.R., 2006. Supplementary Environment Effects Statement, Head Technical Report: Nutrient cycling- current conditions and impact assessment. Marine and Freshwater Systems Report Series No. 17. Primary Industries Research Victoria, Queenscliff. Longmore, 2010. DPI Phytoplankton Data 1987 – 1996

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Longmore, A.R., Cowdell, R.A. and Flint, R. 1996. Nutrient Status of the Water in Port Phillip Bay. Technical Report No. 24. Port Phillip Bay Environmental Study. CSIRO. Yarralumba, ACT. August. Longmore, A. and Nicholson, G. 2010a. Baywide Nutrient Cycling (Denitrification) Monitoring Program- Milestone Report No. 8 (Oct.-Dec. 2009). Fisheries Victoria Technical Report Series No. 88, February 2010. Department of Primary Industries, Queenscliff, Victoria, Australia. 52 pp. Longmore, A. and Nicholson, G. 2010b. Baywide Nutrient Cycling (Denitrification) Monitoring Program- Milestone Report No. 10 (February–June 2010). Fisheries Victoria Technical Report Series No. 109, August 2010. Department of Primary Industries, Queenscliff, Victoria, Australia. 47 pp. Magro, K., Arnott, G. and Hill, D., 1997, Algal blooms in Port Phillip Bay from March 1990 to February 1995: Temporal and spatial distribution and dominant species, Port Phillip Bay Environmental Study, Technical Report No.27, CSIRO, Melbourne.

Mickelson, M. 1990. Dissolved oxygen in bottom waters of Port Phillip Bay. Environmental Services Series No. 90/010, Melbourne and Metropolitan Board of Works, Melbourne. MMBW/FWD 1973. Environmental study of Port Phillip Bay. Report on phase 1, 1968-1971. Melbourne and metropolitan Board of Works and Fisheries and Wildlife Department of Victoria, Melbourne. 372 pp. Mooney, B and de Salas, MF and Hallegraeff, GM and Place, AR, 2009, Survey for karlotoxin production in 15 species of gymnodinioid dinoflagellates (Kareniaceae, Dinophyta), Journal of Phycology, 45, (1): 164-175. Murray, A. and Parslow, J., 1997, Port Phillip Bay Integrated Model: final report. Technical Report No. 44, CSIRO Port Phillip Bay Environmental Study, ACT. Parsons, TR, Maita, Y. and Lalli, CM 1984. A manual of chemical and biological methods for seawater analysis. Pergamon, Oxford, UK. 173 pp. Parsons, M. and Dortch, Q., 2002, Sedimentological evidence of an increase in Pseudo-nitzschia (Bacillariophyceae) abundance in response to coastal eutrophication. Limnol. Oceanogr., 47(2): 2002, 551– 558 PoMC 2008. Water Quality Progress Report #1- 6 – Zinc and Ammonium Assessment, 15 July 2008, Port of Melbourne Corporation. PoMC 2009a. Algal Blooms-Detailed Design CDP_ENV_MD_012_Rev 3.0, Port of Melbourne Corporation.

PoMC 2010a. Water Quality – Detailed Design CDP_ENV_MD_023 Rev 5.0, Port of Melbourne Corporation. Post, A.F., Dubinsky, Z., Wyman, K. and Falkowski, P. G., 1984, Kinetics Of light-intensity adaptation In a marine planktonic diatom, Marine Biology, 83: 231–238.

Seitzinger, S., Harrison, J.A., Bohlke, J.K., Bouwman, A.F., Lowrance, R., Peterson, B., Tobias, C., van Drecht, G. 2006. Denitrification across landscapes and waterscapes: a synthesis. Ecological Applications 16, 2064-2090. Sgrossa, S., Esposito, F. and Montresor, M., 2001, Temperature and daylength regulate encystment in calcareous cyst- forming dinoflagellates, Marine Ecology Process Series 211: 77 – 87. Sokolov, S. 1996, Inputs from the Yarra River and the Patterson River/Mordialloc Main Drain into Port Phillip Bay, Port Phillip Bay Environmental Study, Technical Report No. 33, CSIRO, Melbourne. Sokolov, S. and Black, K.P. 1999. Long-term prediction of water quality for three types of catchment. Marine and freshwater Research 50, 493-502.

Walker, 2009, Victorian Marine Biotoxin Management Plan, Third Edition, Fisheries Victoria. Wood, M. and Beardall, J., 1992, Phytoplankton Ecology of Port Phillip Bay, Victoria, Port Phillip Bay Environmental Study, Technical Report No.8, CSIRO, Melbourne.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

APPENDIX 1 - BACKGROUND EPA’s Role in Monitoring Water Quality in Port Phillip Bay

EPA Victoria has been monitoring the water quality of Port Phillip Bay (PPB) since 1975 with the Marine Fixed Sites Program commencing in 1984. The aims of this monitoring are to: • Identify any long term trends in water quality • Assess the general condition of PPB • Assess the success of management actions through the compliance with environmental objectives. This program has been extensively reported; most recently including an assessment of the long-term trends in nutrient status and water clarity from 1984 to 1999.1 Inputs or loads of freshwater, nutrient and sediment to PPB are reasonably well understood. These inputs enter primarily from several rivers, most notably the Yarra, smaller streams, about 350 storm water drains and two sewage treatment plants (STPs) — Western Treatment Plant (WTP) at Werribee and at Altona. Groundwater discharge into PPB is considered insignificant. Within PPB, nutrient and sediment concentrations can vary greatly. Spatially, concentrations are usually greater inshore or adjacent to major inputs.1 State environment protection policy (Waters of Victoria) (SEPP (WoV)) Schedule F6 Waters of Port Phillip Bay, declared in 1997 is a comprehensive policy framework for the protection of water quality in PPB.2 A key component of SEPP (WoV) is the identification of beneficial uses that the community want to protect and which are used as the basis for maintaining environmental quality. The beneficial uses identified for marine waters including the waters of PPB are: • Maintenance of natural aquatic ecosystems • Water based recreation • Production of molluscs for human consumption • Commercial and recreational use of edible fish and crustacea • Industrial water use • Navigation and shipping. Within PPB, six (regional) segments are recognised. These are: • Hobsons Segment: includes the mouth of the Yarra River and the City of Melbourne and its port facilities • Werribee Segment: the part of PPB adjacent to the WTP outfalls • Corio Segment: All waters in Corio Bay • Inshore Segment: covering all waters within 600m of low tide • Aquatic reserves: those parts of the Bay afforded statutory protection as ‘protected areas’ • General Segment: all other waters in PPB.

1 EPA 2002. Port Phillip Bay Water Quality. Long-term Trends in Nutrient Status and Clarity 1984–1999. EPA Publication 806. 2 EPA Victoria 1997, Variation of the State environment protection policy (Waters of Victoria) - insertion of schedule F6. Waters of Port Phillip Bay. Victorian Government Gazette S 101.

These segments reflect the different types and conditions of environments, surrounding land uses and major inputs, and therefore have different beneficial uses requiring protection. A separate SEPP (WoV) Schedule F7 Waters of the Yarra Catchment provides the policy framework for the protection of water quality in the Yarra River.3 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 environment in PPB. Specific objectives are set for each segment and are shown in Table A1.1. As not all toxicant objectives are set in the SEPP, the Australian and New Zealand Environment Conservation Council (ANZECC) trigger values are used as the default SEPP (WOV) objectives (Table A1.1).4 EPA has historically sampled water quality approximately monthly at six fixed sites in PPB (see Appendix 2, Table A2.1 for details): • Hobsons Bay • Central Bay • Long Reef • Corio Bay • Dromana • Patterson River. Historically, Central Bay and Dromana were considered reference sites for the purpose of calculating nutrient and suspended sediment trigger values. Information relating to coastal land use developments adjacent to Dromana indicates that this site is also likely to be influenced by various human activities similar to the other four sampling sites: • Hobsons Bay site is approximately 800m from shore and is primarily influenced by discharge from the Yarra River • Long Reef site is located approximately 1km from the WTP • Patterson River site is located about 300m from shore and to the south of Patterson River • Corio Bay site is close to domestic and industrial inputs to Corio Bay. As part of the establishment of the Water Quality component of the Channel Deepening Baywide Monitoring Programs (CDBMP) for the CDP, five additional sites to improve the spatial coverage across key areas of PPB augmented EPA’s water quality monitoring program. These additional sites are: • Yarra River at Newport • PoM DMG • Middle Ground Shelf • Sorrento Bank, • Popes Eye. The location of all 11 sampling sites for the Water Quality Baywide Monitoring Program (WQBMP) is provided in Figure 1.

3 EPA Victoria 1999. Variation of the state environment protection policy (Waters of Victoria) - insertion of schedule F7. Waters of the Yarra catchment. Victorian Government Gazette S 89. 4 ANZECC 2000. Australian and New Zealand Guidelines for Fresh and Marine Water Quality (2000), Australian and New Zealand Environment Conservation Council.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Table A1.1 SEPP (WoV) objectives and ANZECC trigger values

Dissolved Oxygen Attenuation Turbidity Suspended Chlorophyll-a Policy Categories (% saturation) of PAR (NTU) Solids (mg/L) (ug/L)

SEPP (WoV) ANZECC Sampling Site schedule & Level of

segment Protection g/L) g/L) µ µ g/L) g/L) g/L) µ µ g/L) µ g/L) µ g/L) g/L) µ µ µ TBT ( Mercury ( Nickel ( Zinc ( Min for Min for surface1m below Min 1m above bottom limitLower for percentile90th Min percentage concentration Salinity variation ( oC) Temperature Secchi disc (m)depth Annual 90th percentile Annual 50th percentile Annual 90th percentile Annual 50th percentile Annual 90th percentile Annual median Annual 90th percentile Arsenic ( ( Cadmium Chromium ( ( Copper ( Lead

>90%>90% N ± 5% N ± 1 >2 0.5 2.5 4.0 <3 <5.5 <5 <1.3 <4.4 <0.4 <70 <10 <0.006 Yarra River at F6 Hobsons Newport >60% N + 2 <20 <50 <25 <60 <13 <0.2 <1 <1.3 <3.4 <0.05 <11 <8 <0.006 F7 Yarra Port

95% >90% >90% N ± 5% N ± 1 >2 0.5 2.5 4.0 <3 <5.5 <5 <1.3 <4.4 <0.4 <70 <10 <0.006 Hobsons Bay F6 Hobsons

>90% >90% N ± 5% N ± 1 >3 0.45 1.5 2.5 <3 <5.5 <5 <1.3 <4.4 <0.4 <70 <5 <0.006 Corio Bay F6 Corio

>90% >90% N ± 5% N ± 1 >3 0.45 2.5 4.0 <3 <5.5 <5 <1.3 <4.4 <0.4 <70 <5 <0.006 Long Reef F6 Werribee

>90% >90% N ± 5% N ± 1 >4 0.35 1.0 2.0 <3 <0.15 <5 <0.3 <2.2 <0.1 <7 <5 <0.0004 Central Bay F6 General

>90% >90% N ± 5% N ± 1 >4 0.35 1.0 2.0 <3 <0.15 <5 <0.3 <2.2 <0.1 <7 <5 <0.0004 PoM DMG F6 General

>90% >90% N ± 5% N ± 1 >3 0.45 1.5 2.5 <3 <0.15 <5 <0.3 <2.2 <0.1 <7 <5 <0.0004 Patterson River F6 Inshore

99% >90% >90% N ± 5% N ± 1 >3 0.45 1.5 2.5 <3 <0.15 <5 <0.3 <2.2 <0.1 <7 <5 <0.0004 Dromana F6 Inshore

Middle Ground >90% >90% N ± 5% N ± 1 >4 0.35 1.0 2.0 <3 <0.15 <5 <0.3 <2.2 <0.1 <7 <5 <0.0004 Shelf F6 General

>90% >90% N ± 5% N ± 1 >4 0.35 1.0 2.0 <3 <0.15 <5 <0.3 <2.2 <0.1 <7 <5 <0.0004 Sorrento Bank F6 General

>90% >90% N ± 5% N ± 1 >4 0.35 1.0 2.0 <3 <0.15 <5 <0.3 <2.2 <0.1 <7 <5 <0.0004 Popes Eye F6 General

SEPP Schedule F6 - Waters of Port Phillip Bay, and SEPP Waters of Victoria Limit of reporting above SEPP objective SEPP Schedule F7 - Waters of the Yarra Catchment objectives

N=natural background ANZECC trigger values not highlighted Limit of reporting above ANZECC trigger value

Notes Schedule F7 (Waters of the Yarra Catchment) is included for comparison of water quality objectives at the Yarra River at Newport site, as this site has been determined to be in a crossover area between schedules F6 and F7. Both schedule segments can be applicable to the site dependent on tide cycle and flow conditions in the Yarra mouth

APPENDIX 2 - METHODS Sampling Locations

The Water Quality Monitoring Program sampling schedule is monthly, at 11 fixed sampling sites across PPB (Figure 1). Table A2.1 provides further information relating to the selection of the sites and corresponding SEPP (WoV) segments. Table A2.1 Locations and corresponding SEPP (WoV) segments Site Site no. Historical Segment Purpose name (PoMC) Data Yarra This samples Yarra River water prior to entering PPB. Sediments Port PoMC data Yarra here contain contaminants that 2004-2005 River at 8005 segment may be mobilised by storms, and 2006- Newport of shipping and dredging. It is near 2007 Schedule a popular fishing area known as F6/F7* the ‘Warmies’. Hobsons PoMC 2004- Hobsons Bay is a recreational segment 5 and 2006- area and home to a Little Hobsons 7007 of 7. ; EPA Penguin colony. It is the interface Bay Schedule 1994 to between the Yarra River and F6 present PPB. Corio EPA 1994 - This is a recreational area and Corio Bay 4321 (F6) present supports seagrass beds. This area is influenced by the Long Werribee EPA 1994 - WTP. Links to other Baywide 4310 Reef (F6) present Monitoring programs in same area. General, EPA 1994- bordering 1996 This is an important recreational Dromana 2808 ‘Inshore’ and2005 - area. (F6) present General, EPA 1994- This site is near Patterson River Patterson bordering 4604 1996 and which is a significant input to River ‘Inshore’ 2005-present PPB. (F6) This is at the centre of the PoM Dredged Material Ground, to PoM confirm that placement and 4503 General DMG storage of contaminated material does not result in significant impacts to water quality. EPA 1994 – present. This site is indicative of water quality across large central area Central PoMC 4514 General of PPB. Links to other Baywide Bay nearby (4519) 2004- Monitoring programs in same 2005 and area. 2006-2007 Nearby This is on the edge of the Great Middle (2710) PoMC Sands area. Links to other Ground 2719 General 2004-2005 Baywide Monitoring programs in Shelf and 2006- same area. 2007 Key recreational area and PoMC 2004- Sorrento seagrass beds. Links to other 2006 General 2005 and Bank Baywide Monitoring programs in 2006-2007 same area. This is near the boundary of a PoMC 2004- Popes marine national park, and is 2301 General 2005 and Eye strongly influenced by tidal 2006-2007 exchange with Bass Strait.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

*There is an anomaly within the northern boundary of SEPP (WoV) Schedule F6 such that the latitude/longitude puts the ‘Yarra River at Newport’ site in the Hobsons segment, whereas ‘Eastings and Northings’ put this site in Schedule F7 Yarra Port segment. For the purpose of this report, objectives for both Schedules F6 and F7 values are considered for the Yarra site, although for Progress Reports # 1 & 2, only Schedule F6 values were considered.

Field Sampling

EPA personnel or contractors, who are trained in the sampling methodology, conduct all field sampling. Fieldwork involves both in-situ monitoring and the collection of water samples for laboratory analysis.

A summary of the methods for in-situ monitoring and the collection of water quality and algal samples are provided below. Descriptions of the methods are provided in the following EPA Standard Operating Procedures (SOPs): • In-situ Monitoring • Water Quality Sampling • Algal Sampling • Sample Handling and Custody. Detail on sample and equipment preparation is also contained in the SOPs. This includes sourcing sample containers from laboratories, marking up sample containers, checklists for equipment and supplies and equipment maintenance and inspection. The SOPs are incorporated into the Quality System for delivery of the WQBMP.

Field sampling is undertaken monthly within a 2-week window starting from the second week of the month. This is preferably conducted over three consecutive days, however flexibility in timing is required due to logistical and OH&S constraints.

In-situ Monitoring A CTD Profiler is used to measure the in-situ parameters at each site including conductivity, depth, temperature, dissolved oxygen (% saturation), photosynthetic active radiation (PAR), fluorescence and turbidity. A Secchi disc and measured line is used to measure Secchi disc depth. Further detail on operation, calibration and QC checks for the CTD profiler are provided in the ‘In-situ Monitoring’ SOP.

Water Quality

Water samples are collected using a peristaltic pump with medical grade silicone tubing. Samples are collected at the near surface (~0.5 m) of the water column and sub-samples withdrawn for total nutrients, total metals, TBT and suspended solids. Sub-samples are filtered through 0.45µm membrane filters and stored for dissolved nutrient and dissolved metal analysis. Chlorophyll-a samples are collected by gravity filtration of seawater through a glass fibre filter, and stored on ice. The need for a bottom water sample is determined based on whether salinity stratification (a change with depth of more than 10psu) is identified by the CTD profiler.

Sample containers, sampling and preservation methodologies, and sample handling and storage are provided in the ‘Water Quality Sampling’ SOP.

Algal Sampling

At each site an integrated water sample is taken for algal enumeration and a net tow sample is collected for algal identification. Full detail including sample containers, sampling and preservation methodologies and sample handling and storage is provided in the ‘Algal Sampling’ SOP.

Sample blanks and replicates

Field sampling quality control measures include the collection of field blanks and replicates. This includes:

• Two freshwater field blanks per cruise to test for contamination during sample collection/ treatment/ storage. • Two field replicates to test for contamination during sample collection/treatment/storage, site heterogeneity and laboratory precision. These are two randomly selected sites per monthly sampling cycle in each of the north and south of PPB, and are analysed for each of the parameters normally tested for each location. Replicate sample sites are selected in advance on a random basis so they will remain blind as far as the laboratories are concerned. Where a replicate is taken, a filtered replicate is also collected for required parameters.

Sample handling and custody

Sample storage requirements and holding times are provided in the ‘Sample Handling and Custody’ SOP. Chain of Custody forms accompany all samples.

Quality Assurance for field sampling

The EPA Quality Plan5 is the key document that outlines all relevant QAQC specifications for the EPA WQBMP. This includes the QAQC requirements for the fieldwork as outlined below. QA/QC for fieldwork includes:

• Sampling for metals, nutrients and TBT is carried out using powder-free, plastic disposable gloves to minimise contamination • Sampling equipment is left open to the water column for approximately five minutes allowing it to sufficiently rinse prior to taking a sample • All samples are stored on ice and transported to the laboratories within 24 hours of sample collection • Collection of field blanks and replicates as described in Section 2.1.4 • The EPA Field Scientist provides field records for the CTD profiler to the EPA Project Manager for the QA file including serial number, when new equipment is used, where used and details of calibration checks. These records will show if any clear ‘steps’ in the data can be tracked and attributed to changes in instrumentation, • Chain of Custody forms are created and forwarded with the samples to the laboratories.

5 EPA 2010, EPA Victoria Baywide Water Quality Monitoring Program Quality Plan

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Laboratory Analysis

The laboratory analysis of samples is contracted to Ecowise Australia for metals and TBT analysis, Department of Primary Industries (DPI) Queenscliff for nutrients (and some physico-chemical parameters) and MicroAlgal Services for algal analysis. DPI Queenscliff analyses samples for physico-chemical parameters such as suspended solids, dissolved oxygen, salinity, dissolved nutrients, total N and P, particulate N (and dissolved organic N), silicate and algal pigments (chlorophyll-a and phaeophytin-a).

Reports are provided by the laboratories detailing their QAQC programs while the EPA also undertakes internal QAQC to ensure quality control for laboratory results.6

Data Assessment Methods

In order to detect changes in water quality outside expected variability in PPB, two control charting techniques (CSIRO/Emphron 2007)7 have been employed in the analysis of the WQBMP results: • An Exponentially Weighted Moving Average (EWMA) control chart is used for assessment of longer-term changes in baseline results for nutrients, total metals and chlorophyll-a. The EWMA is a statistic that averages the data in a way that gives less weight to data as they are further removed in time. To do this EWMA applies weighting factors which decrease exponentially over time. This gives relatively greater importance to recent observations while still not discarding older observations entirely. EWMA is being used in this context to detect persistent changes from a baseline ‘target’ concentration, usually the historical mean of the data, which may reflect long term changes in water quality. An upper control limit for the EWMA has been calculated to assist in deciding whether a persistent change from the target value may have occurred (Table A2.2). • A Shewhart control chart is used to detect changes in the number or size of peak events for nutrients, total metals and TBT. These changes will reflect short-term changes in water quality (Table A2.3).

6 EPA 2010, EPA Victoria Baywide Water Quality Monitoring Program Quality Plan 7 CSIRO/Emphron 2007. Channel Deepening Project Bay-Wide Monitoring Programme Water Quality, Emphron Informatics Pty Ltd, December 2007.

Table A2.2 EWMA control limits for listed water quality parameters

Nitrate plus Total Ammonium Total Nitrogen Phosphate Sampling site Nitrite Phosphorus Chlorophyll-a Arsenic µg/L µg/L µg/L µg/L µg/L µg/L µg/L Yarra River at Newport 32.42 39.52 278.39 86.19 108.01 2.0 3.23 Hobsons Bay 19.45 39.53 266.22 85.72 105.32 3.9 2.98 Central Bay 9.90 3.61 168.10 72.32 84.08 1.1 2.86 PoM DMG 6.16 9.92 176.47 66.31 83.99 1.0 3.10 Corio Bay 10.70 2.31 224.48 100.12 115.66 1.4 3.66 Long Reef 219.05 83.74 629.12 238.83 305.50 6.8 3.20 Patterson River 13.65 42.75 243.10 69.75 89.34 2.2 2.59 Dromana 5.00 4.29 170.20 56.93 70.12 1.6 2.52 Middle Ground Shelf 7.02 2.29 156.09 50.94 63.85 0.8 N/A Sorrento Bank 8.16 4.93 143.10 36.40 45.74 0.8 N/A Popes Eye 8.20 12.73 145.12 36.75 120.94 0.8 N/A

Notes NA – Not available due to lack of historical data.

Source: Table 4 CDP_ENV_MD_023 Rev 5.0 (available on the CDP website www.channelproject.com).

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Table A2.3 Shewhart control limits for listed water quality parameters

Total Nitrate Total Sampling site Nitrogen Ammonium plus Phosphorus Phosphate Arsenic Cadmium Chromium Copper Lead Mercury Nickel Zinc TBT Nitrite µg/L µg/L µg/L µg/L µg/L µg/L µg/L µg/L µg/L µg/L µg/L µg/L µg/L µg/L Yarra River at Newport 383.31 88.78 182.90 138.91 107.54 4.75 0.20 0.58 3.08 2.79 0.10 4.29 12.77 0.02 Hobsons Bay 382.82 50.61 257.50 135.51 129.08 4.43 0.25 1.17 1.70 0.95 0.13 2.28 9.13 0.01 Central Bay 206.91 21.50 7.43 106.48 112.50 4.66 * * * * * 1.95 * * PoM DMG 217.07 7.81 28.33 107.98 76.61 4.73 * * * * * 2.82 * 0.02 Corio Bay 275.74 25.37 5.00 140.27 127.68 5.57 * NA * * * 1.90 * NA Long Reef 1035.88 999.28 512.03 536.16 445.31 4.56 * NA * * * 2.17 * NA Patterson River 367.57 30.57 366.52 111.81 87.58 3.56 * NA * * * 1.14 * NA Dromana 222.84 11.03 5.71 89.64 75.42 3.58 * NA * * * 1.06 * NA Middle Ground Shelf 185.93 10.66 2.71 96.82 65.33 NA NA NA NA NA NA NA NA NA Sorrento Bank 168.74 11.54 9.50 63.20 48.44 NA NA NA NA NA NA NA NA NA Popes Eye 209.84 14.74 42.71 471.38 148.04 NA NA NA NA NA NA NA NA NA

Notes NA – Not available due to lack of historical data. * - No limit, as more than half historical data is below limits of reporting.

Source: Table 5 CDP_ENV_MD_023 Rev 5.0, (available on the CDP website www.channelproject.com)

EWMA and Shewhart charts have been generated for all parameters with chart-based limits specified in Tables A2.2 and A2.3 respectively. Exceedence of these limits flag results as being outside of normal background variability based on historical data. The next question is to determine whether results are also outside of ’expected variability’, based on the predicted effects of the CDP as defined in the SEES. Where results are considered to be outside expected variability, EPA/PoMC leads an assessment of the significance of the result to the environment. If results are significant, this initiates further risk-based assessments by PoMC in accordance with the Water Quality Detailed Design CDP_ENV_MD_023_Rev 5.0, Decision Framework for Management. 8 In cases where no Shewhart limits exist (asterisks in Table A2.3), SEPP (WoV) objectives, or ANZECC ‘trigger values’ where no SEPP (WoV) objectives exist (Table A1.1), are used for comparison. Monthly progress reports and six monthly milestone reports also include a discussion of all applicable results compared to SEPP (WoV) as a general observation of water quality at the program’s monitoring sites.

In some cases, for example nutrients, SEPP (WoV) objectives do not exist but EWMA and Shewhart limits have been derived. In other cases (e.g. some metals), either SEPP (WoV) objectives are explicit or, by default, ANZECC trigger values are used. For most metals and sites there is insufficient historical data to derive Shewhart or EWMA limits. Interpretation of the algal analysis (species composition and enumeration) is defined in the Algal Blooms Detailed Design CDP_ENV_MD_012_Rev 3.0.9 Algal results are compared against a threshold as a tool to identify change outside of expected variability. The minimum warning levels used in the Victorian Shellfish Operations Manual (VSOM) for toxic and nuisance species have been adopted as the threshold concentrations. These are listed in Section 4.2.1 of the Algal Blooms Detailed Design. The Algal Blooms Detailed Design also defines the method for interpreting chlorophyll-a results using an EWMA and associated limits. Another requirement of the Water Quality Detailed Design is the inclusion of summary statistics, particularly as they relate to some SEPP (WoV) water quality parameter requirements for comparison with annual statistical derivations such as median and percentiles. When calculating summary statistics, if a value is less than the limit of reporting (LOR) then it is not possible to calculate a mean. When calculating percentiles, including the median, values less than LOR are temporarily replaced with a number that is marginally less than the LOR so as to make it distinguishable from the LOR itself (e.g. replace <0.2 with 0.199). The percentiles and median are then calculated and any estimates that are smaller than the LOR are replaced with '

External Data Sources

This report also includes data from concurrent water quality monitoring activities undertaken in PPB and the surrounding catchments, in addition to historical datasets. The water quality monitoring program provides monthly snapshots of the bay conditions, while the in-situ continuous measurements help fill the gaps to understand prevailing dynamics affecting water quality. Historical and other data sets assist with understanding the external influences and historical conditions.

As part of the Port Phillip Bay Environmental Management Plan (PPB EMP) continuous instrumental measures of temperature, salinity dissolved oxygen and chlorophyll fluorescence have been maintained by DPI at three mooring locations in PPB since 2002. These are located at:

8 PoMC 2010. Water Quality – Detailed Design CDP_ENV_MD_023 Rev 5.0, Port of Melbourne Corporation. 9 PoMC 2009. Algal Blooms – Detailed Design CDP_ENV_MD_012 Rev 3.0, Port of Melbourne Corporation.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

• Hobsons Bay

• Central Bay

• Long Reef A fourth site located in the south at Middle Ground Shelf was added in 2007 to augment this network for the CDP nutrient cycling monitoring program. At each of these four monitoring sites, instruments collecting hourly data are located at near surface (~3m) and near bottom. Site locations are shown in Figure A2.1 and further details of their configuration and data capture are provided in PoMC (2010).10 The near-surface (3m) sensor data is presented in the following results section with comparative results from the monthly water quality monitoring program data. Figure A2.1 DPI Nutrient cycling continuous in-situ monitoring sites

Source: PoMC 2010 Nutrient Cycling Detailed Design CDP_ENV_MD_019 Rev 5.0, Port of Melbourne Corporation.

To improve both spatial and temporal coverage of water quality conditions, EPA installed a marine monitoring system on the ‘Spirit of Tasmania 1’ in 2008. This monitoring system measures water quality in PPB and the background oceanic influences of Bass Strait. The system became operational in September 2008 and provided an unbroken record through to July 2009, when the vessel was taken out of service. The

10 PoMC 2010. Nutrient Cycling Detailed Design CDP_ENV_MD_019 Rev 5.0, Port of Melbourne Corporation.

system was back in service in September 2009 and has been operational to the end of the current reporting period. The Spirit of Tasmania 1 travels from Melbourne to Devonport daily. On each daily crossing the in-situ monitoring system samples surface waters (0-6m deep) as ten second averages of salinity, temperature, chlorophyll-a fluorescence, turbidity, and position. Travelling at approximately 20 knots this corresponds to sample “grabs” at every 100m along the ship track. Sampling at high frequency significantly improves the capability to resolve ecosystem dynamics in PPB. An example of daily shiptrack and sensor data is shown in Figure A2.2. Figure A2.2 Examples of IMOS shipborne data sampled from the Spirit of Tasmania.

This marine monitoring system is part of the “Ships of Opportunity” facility incorporated within the national Integrated Marine Observing System (IMOS).11 Data (and associated metadata) for all IMOS observations is available to support other researchers and end-users at IMOS (2010).12

11 IMOS 2010. Integrated Marine Observing System, http://www.imos.org.au. 12 IMOS 2010. Integrated Marine Observing System, Available Spirit of Tasmania 1 data from the IMOS data server, http://opendap-tpac.arcs.org.au/thredds/catalog/IMOS/SOOP/SOOP-TMV/VLST_Spirit-of-Tasmania- 1/transect/catalog.html.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

The data sampled from the Spirit of Tasmania 1, is referred to in this report as IMOS shipborne data. Contoured sensor data is presented in the following results section as shiptrack distance in PPB (from Port Melbourne Pier) against date. Each plot represents data from approximately 100 Bass Strait crossings. Additional data on trace heavy metals is also sourced from the EPA extended beach monitoring program, the PoMC maintenance dredging beach monitoring program, and the Melbourne Water, water quality monitoring program. EPA has been monitoring beach water quality for many years as part of the summer Beach Report program. In March 2008, responding to increased community interest, the beach water quality monitoring program was extended to operate for a full year and include a wider range of water quality indicators. The program monitored 36 beaches around the Bay (Figure A2.3).The program monitored enterococci, algae, heavy metals and organic chemicals on a weekly basis from March 2008 to September 2009 at 36 beaches around the Bay (Figure A2.3).13 As part of the PoMC routine maintenance dredging program, water from six northern PPB beaches was monitored for heavy metals (Figure A2.3). The monitoring program commenced on 17th November 2009 with weekly testing concluding in June 2010.14 Melbourne Water conducts water quality monitoring at 136 sites along rivers and creeks in the Port Phillip and Western Port region. The program monitors a range of water quality indicators including heavy metals and nutrients. The program is designed to assess broad-scale, long-term trends in water quality (typically over eight to 10 years) and to assess progress against SEPP objectives.15 Figure A2.3 EPA and PoMC Beach monitoring sites

13 EPA 2009. Extended Monitoring of Beach Water Quality in Port Philip Bay – March 2008 – September 2009. 14 OEM 2010. www.oem.vic.gov.au/Maintenancedredging. 15 MW 2010. www.melbournewater.com.au/content/rivers_and_creeks/river_health/water_quality_monitoring.

Further data sets that have been included in this report include the data collected from the annual Two Bays monitoring program16 and historical phytoplankton data collected by DPI from 1987-199617. The Two Bays monitoring program undertaken in January 2010, survey along the coast of PPB using continuous loggers. The water quality parameters monitored include nutrients (total nitrogen and total phosphorous) and physico chemical parameters (salinity, temperature, turbidity and fluorescence). Historical phytoplankton data collected by DPI includes all phytoplankton species identified and counted on a fortnightly basis from 1987- 1996 at numerous sites across PPB.

16 Two Bays 2010 http://www.svpelican.com.au/brain/twobays/2010/index.html 17 DPI phytoplankton data was made available through Andy Longmore.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

APPENDIX 3 - RESULTS

This Milestone Report (#6) incorporates all data collected since the inception of the program in November 2007 with the focus primarily on this reporting period extending from January – June 2010.

Field Sampling

Field sampling was conducted monthly as outlined in Table A3.1. The maintenance dredging program, using a backhoe/grab dredge, commenced on the 17th November 2009 in the Yarra River and Hobsons Bay and was completed mid 2010. Table A3.1 Field sampling dates and weather conditions (January – June 2010) Progress Report Sampling Dates Weather Observations 13th January Moderate to strong 15-20kt winds increasing to 20-25kts; waves 0.7-1.2m

No.25 14th January Light 5-10kt winds increasing to 20-25kts; waves 0.2-1.5m Moderate 10-15kt winds; waves 0.5m 15th January Hobsons Bay very turbid Light 0-5kt winds increasing to 10-15kts; waves 0.1-0.3m 10th February Yarra River turbid Light rain Light 0-5kt winds increasing to 15-20kts; waves 0-1.5m No.26 11th February Heavy rain Moderate 10-15kt winds increasing to 20-25kts; waves 0.4-1.0m 12th February Light rain Slack water at Sorrento and strong ebb tide at Popes Eye Light 0-5kt winds increasing to 5-10kts; waves 0.1-0.4m 12th March Strong ebb tide in south of PPB No.27 14th March Light 5-10kt winds; waves 0.2m 15th March Light 5-10kt winds decreasing to 0-5kts; waves 0.3m Moderate to strong 10-20kt winds decreasing to 5-10kts; waves 0.5-0.8m 14th April Moderate to strong flood tide at Popes Eye and Sorrento No.28 15th April Moderate 10-15kt winds; waves 0.5m 16th April Light 5-10kt winds; waves 0.2m Moderate 10-15kt winds; waves 0.3-0.4m 13th May End of flood tide at Sorrento and slack water at Popes Eye

No.29 14th May Light 5-10kt winds; waves 0.4m 17th May Calm 18th May Light 0-5kt winds; waves 0-0.2m Light 0-5kt winds; waves 0.2m 21st June Flood tide at MGS No.30 Light 0-5kt winds; waves 0.3m 22nd June Slack water at Sorrento and 1st half of ebb tide at Popes Eye 23rd June Light 0-5kt winds increasing to 10-15kts; waves 0.2-0.4m

Quality Assurance/Control (QA/QC) Field and laboratory QA/QC data and discussion relevant to this reporting period are provided in Appendix 4.

Exception reports

A number of deviations from the Detailed Design occurred during the reporting period. Formal exception reports were provided with progress reports as a means of documenting events on each occasion. These exception reports are referenced in relevant progress reports and help ensure that learning’s are captured and improvements incorporated back into the program. All exception reports from this reporting period are summarised in Table A3.2. Table A3.2 Summary of Exception Reports (January – June 2010) Report Number Exception A number of errors were identified in the reporting of phytoplankton data including: - Total phytoplankton cell counts were incorrectly reported in Tables 4 and 8 of Progress Report #19 (July 2009). ER100101 - The Long Reef dinoflagellate cell count was incorrectly reported in Tables 4 and 8 of Progress Report #16 (April 2009). - Progress Report #11 (November 2008) and #20 (August 2009) are missing data for Popes Eye in Table 8. EWMA NOx values for Long Reef and Corio Bay were incorrectly reported in Progress Reports ER100102 #23 (November 2009) and #24 (December 2009). ER100103 No reliable lead data for Hobsons Bay is available for January 2010.

ER100301 No reliable data is available for filtered chromium, nickel and zinc at Central Bay in March 2010.

The summary statistics in Milestone Reports No 4 and 5 did not include the 10th and 95th ER100401 percentile values.

Results from Progress Reports

This subsection presents and discusses the data collected from field sampling events carried out from January – June 2010, as outlined in Progress Reports # 25 -3018, meteorological data and additional external data sources. The information in this subsection highlights exceedences of the program’s control limits (EWMA and Shewhart), the criteria used to flag possible variation from historical water quality data. Secondary comparison with SEPP (WoV) F6 and F7 objectives, or ANZECC trigger values as applicable, are also made to assist broader interpretation of the results. This section is presented according to the water quality parameter categories: • Physico-chemical data • Phytoplankton and Algal Pigments • Nutrients • Metals.

18 EPA 2010. Baywide Water Quality Monitoring Program Progress Reports No 25-30, January – June 2010.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Where appropriate, results are also charted in the context of the Shewhart and EWMA control limits, SEPP/ANZECC values and historical means. Tables A3.3 summarises all exceedences of EWMA and Shewhart control limits observed during the reporting period for physico-chemical data/nutrients and metals, respectively. These tables also include exceedences of SEPP/ANZECC objectives where no Shewhart limit is available. Assessment by the PoMC of these exceedences in terms of any implications for the ecological health of PPB and subsequently the management of this project are presented in Appendix 5, Results outside of natural/ expected variability.

Summary statistics are provided for relevant metals, nutrients and physico-chemical parameters for comparison against SEPP (WoV) F6 and F7 objectives, or ANZECC trigger values (see Appendix 6). A minimum of 11 (monthly) data points are required to gain a true comparison with SEPP objectives against an annual statistic. Control charts for a number of parameters are presented throughout the results section. The following notes are provided to assist with interpretation: • Where the historical mean is plotted below the limit of reporting (LOR), data without imposed reporting limits was used in calculations. • Legends on control charts. Curr LOR: For all parameters (except Secchi disc depth) the result is below the LOR. For Secchi disc depth the Secchi disc was visible on the bottom. Hist mean: EPA historical mean Hist*mean: Historical mean value was obtained from Emphron (2007)19

19 Emphron Informatics Pty Ltd 2008 Channel Deepening Project Bay-wide Monitoring Programme Water Quality (Report 2007/172)

Meteorological conditions

Rainfall Total rainfall during summer and autumn was close to the long term average across the Melbourne region while rainfall for June was slightly higher than usual (Figure A3.1).This continues the trend seen in the previous reporting period (Figure A3.2) and is in contrast to the below average rainfall seen during the same period in 2009 (Figure A3.3). Autumn 2010 was the wettest autumn Victoria has experienced since 2000.20

Figure A3.1 Victorian rainfall deciles Jan – June 2010

Figure A3.2 Victorian rainfall deciles July – Dec 2009

20 Bureau of Meteorology

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.3 Victorian rainfall deciles Jan - June 2009

Water quality in PPB continues to be influenced by rainfall and associated catchment inputs. The majority of nutrients and toxicants supplied by rivers to PPB are discharged during storms.21 The only storm event, using storm event criteria outlined in Gibbs et al (2007)22, identified for the Yarra River in the last six months occurred on 8th March 2010 (Figure A3.4). The storm event on the 8th March 2010 was a response to the severe thunderstorms associated with large hail and heavy rain on the 6th March 2010. This heavy rainfall (35.8mm) resulted in high mean river flows (1300 – 4940ML/day) for a number of days following the event. Water quality sampling was conducted in the week after this event. The storm event criteria for the Yarra River are that 24-hour rainfall must exceed 20 mm with rainfall continuing and Yarra River flow exceeds 15 m3.s-1 (~ 1,300 ML/day) and is rising. The storm event criterion of 24-hour rainfall exceeding 16mm for Patterson River was exceeded on several occasions during the last six months (Figure A3.5). The storm event on the 12th February coincided with sampling, while the storm event on the 6th March occurred several days prior to the water quality sampling event. The influence of the increased catchment inputs into PPB was detected to some degree by the monthly sampling, with the continuous DPI nutrient cycling and Integrated Marine Observing System (IMOS) data also capturing the changes in water quality (Figure A3.6). Fairfield (river flow) and Viewbank (rainfall) were identified in Gibbs et al (2007) as the most relevant Melbourne Water (MW)23 and Bureau of Meteorology (BoM)24 sites for the Yarra River, while Moorabbin was identified as the most relevant BoM rainfall site for Patterson River.

21 Harris et al 1996, Port Phillip Bay Environmental Study Final Report 22 Gibbs et al 2007 Port of Melbourne Corporation Channel Deepening Project Baseline Water Quality Monitoring 2006- 2007 Marine and Freshwater Systems Report Series No. 22, Primary Industries Research Victoria, Queenscliff. 23 All river flow data obtained from Melbourne Water < www.melbournewater.com.au> 24 All rainfall data obtained from the Bureau of Meteorology

Figure A3.4 Yarra River rainfall, river flow and storm events (January – June 2010)

Figure A3.5 Patterson River rainfall and storm events (January – June 2010)

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.6 IMOS shipborne track data (March 7 - 10 2010)

Air Temperature Minimum and maximum air temperatures for the Melbourne region over the last six months were warmer than usual (Figure A3.7). During summer, minimum and maximum temperatures were on average 1.9-2.4°C warmer than usually experienced, while autumn temperatures were around 1°C warmer and June temperatures were 0.6°C warmer than usual.25 Figure A3.7 Victorian temperature deciles (January – June 2010)

25 Bureau of Meteorology

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.8 Map of WQBMP exceedences (January – June 2010)

Water Quality Monitoring Sites Dredged Material Ground Shipping Channel

Chromium: Toxicants are known to be discharged from Ammonium: Ammonium is present in all natural waters. The Chlorophyll-a: Chlorophyll-a (as an indicator of rivers following increases in catchment flows exceedences at Dromana are considered to be associated phytoplankton biomass) is influenced by temperature, light with stepwise increases since the 1990’s and the relatively and nutrients. High levels of chlorophyll-a are associated with Secchi disk depth: Water clarity can be influenced by a low control limit at this site increased catchment inputs at sites close to nutrient range of natural high river flows, increased phytoplankton discharges in the north and west. Seasonal winter increases biomass and adverse weather conditions NOx: Concentrations of NOx increase at sites close to rivers are observed in the south following rainfall as nutrients are washed from the rivers into PPB Harmful phytoplankton species Dissolved Oxygen: DO concentrations can vary greatly Total Nitrogen: Concentrations of Total Nitrogen increase The distribution of marine phytoplankton is regulated by over a daily period depending on water temperature, following rainfall over the catchment with increases in river chemical, physical and biological conditions. There have salinity, photosynthetic and microbial activity flow, surface runoff and nutrient input into PPB been a number of toxic or nuisance algal blooms in PPB since 1986, including A.catenella and Pseudo-nitzschia spp.

Table A3.3 Summary of exceedence of control limits for physico-chemical data and nutrients (January – June 2010)

Secchi Dissolved Total Date Site Depth disc depth Oxygen Ammonium Nitrate plus Nitrite Total Nitrogen Chlorophyll-a Chromium (m) (m) % sat. (μg/L) (μg/L) μg/L (μg/L) (μg/L) Value EWMA Value EWMA Value EWMA Value1 EWMA 15/01/2010 Yarra River at Newport 0.5 1.8 80.7 343 4.77 3.44 15/01/2010 Hobsons Bay 0.5 1.1 15/01/2010 Long Reef 0.5 2.7 10/02/2010 Yarra River at Newport 0.5 1.3 65.0 322 8.87 4.53 11/02/2010 Corio Bay 0.5 291 3.50 1.48 15/03/2010 Yarra River at Newport 0.5 1.3 84.6 534 364 7.44 5.11 0.6 12/03/2010 Dromana 0.5 5.3 15/03/2010 Corio Bay 0.5 1.64 15/03/2010 Long Reef 0.5 4.92 16/04/2010 Yarra River at Newport 0.5 1.9 86 93.3 442 380 4.41 14/04/2010 Dromana 0.5 5.6 16/04/2010 Corio Bay 0.5 1.53 18/05/2010 Yarra River at Newport 0.5 87 83.5 355 3.89 17/05/2010 Corio Bay 0.5 2.9 225 3.47 1.92 14/05/2010 PoM DMG 0.5 8.5 13/05/2010 Dromana 0.5 6.0 14/05/2010 Patterson River 0.5 2.54 23/06/2010 Yarra River at Newport 0.5 77.4 331 3.66 21/06/2010 Dromana 0.5 5.9 22/06/2010 Corio Bay 0.5 1.77 23/06/2010 Patterson River 0.5 4.94 21/06/2010 Middle Ground Shelf 0.5 0.86 22/06/2010 Sorrento Bank 0.5 0.83

Notes 1. The chlorophyll a value is above the 90th percentile objective in SEPP (WoV) Schedule F6.

Yellow coloured cells indicate measured results above the Shewhart control limit (for ‘total’ fraction). See Table A2.3 for detail.

Orange coloured cells indicate EWMA calculated results above EWMA control limits. See Table A2.2 for detail. Blue coloured cells indicate results outside SEPP (WoV) objectives where a Shewhart limit is not available. See Table A1.1 for detail.

53 BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Water quality in PPB is highly variable as seen by both the WQBMP (Figure A3.8) and the continuous water quality monitoring data collected by the Two Bays program in January (Figure A3.9). Turbidity is highest in Hobson Bay close to the Yarra River while elevated nutrients and chlorophyll fluorescence are found close to coastal discharges including the WTP near Werribee and the Yarra River. During the current reporting period (January – June 2010) the most variable water quality was seen in the north and west of PPB. The greatest number of control limit and SEPP (WoV) exceedences were reported from the Yarra River at Newport while a number of nutrient and phytoplankton exceedences were recorded at Corio Bay. Other sites typically had few or no exceedences. Figure A3.9 Two Bays continuous water quality monitoring measurements (10-23 January 2010)

Physico-chemical data Salinity and Temperature

Salinity and temperature readings from both the EPA water quality (WQBMP) and DPI nutrient cycling (NCBMP) monitoring programs show similar patterns at each of the common sampling sites (Central Bay, Long Reef, Hobsons Bay and Middle Ground Shelf). Water temperature followed predictable seasonal patterns with highest temperatures recorded in February 2010 (Figure A3.10). Water temperatures have since cooled to around 13°C in June, in parallel with decreasing air temperatures.

Figure A3.10 Surface water temperature at Central Bay (January – June 2010)

Temperature Temperature (oC) 15

10 14-10-2009 03-12-2009 22-01-2010 13-03-2010 02-05-2010 21-06-2010 10-08-2010 Date DPI nutrient cycling surface data EPA water quality data (probe) EPA water quality data (CTD)

Water temperatures in February 2010 at most sites were the highest recorded for the WQBMP, particularly at Long Reef, Corio Bay and Hobsons Bay (Figure A3.11). Water temperatures at these sites were 2-4°C higher than those recorded in 2008 and 2009. The warmer temperatures in 2010 are also evident in the IMOS shipborne data when compared to 2009, with warmer temperatures throughout the bay for a longer period of time (Figure A3.12).

Figure A3.11 February surface water temperature across PPB and the Yarra River (2008 – 2010)

Temperature (oC) 15 17 19 21 23 25

Long Reef

Patterson River

Central Bay

Dromana

Corio Bay

Hobsons Bay Site Site

Yarra River at Newport

PoM DMG

MGS

Sorrento Feb 2008 Popes Eye Feb 2009 Feb 2010

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.12 IMOS shipborne water temperature measurements for PPB (August 2008 – July 2009 and September 2009 – June 2010)

Salinity in PPB also follows a seasonal pattern with peaks in salinity generally occurring during the autumn months (Figure A3.13). Due to the return of average rainfall over the last 12 months, the autumn increase in salinity was lower than seen in the drier years of 2008 and 2009. Figure A3.13 Average salinity for PPB (January 2008 – June 2010)

37.5

36.5

36 Salinity (psu) Salinity

35.5

Salinity (all sites) 35 Salinity (exYarra River at Newport)

34.5 Jul-08 Jul-09 Jul-10 Jan-08 Jan-09 Jan-10 Sep-08 Sep-09 Nov-08 Nov-09 Mar-08 Mar-09 Mar-10 May-08 May-09 May-10 Date

The influence of rainfall and associated catchment inputs on salinity is most evident at sites close to rivers (Yarra River at Newport, Hobsons Bay (Figure A3.14) and Patterson River) and also at Long Reef in the vicinity of the WTP. NCBMP data from Hobsons Bay (Figure A3.14) and Long Reef and CTD profile data from the WQBMP at the Yarra River at Newport site (Figure A3.15) and Patterson River show the influence of freshwater, with lower salinity recorded in surface waters (e.g. 28-35 psu). In contrast, salinity at the entrance to the Bay is influenced by Bass Strait with salinity levels closer to 35 - 36 psu, and is more consistent with depth (Figure A3.16). Figure A3.14 Hobsons Bay surface and bottom salinity measurements (December 2009 – June 2010)

40 40

38 32

36 24 Salinity (psu) Salinity

34 16 Rainfall (mm)

32 8

30 0 14-10-2009 03-12-2009 22-01-2010 13-03-2010 02-05-2010 21-06-2010 10-08-2010 Date DPI nutrient cycling surface salinity data DPI nutrient cycling bottom salinity data Viewbank Rainfall

Figure A3.15 Yarra River at Newport CTD salinity profiles (January – June 2010)

Salinity (psu) 28 30 32 34 36 38 0

4 Depth (m) Depth 5

Jan-10 Feb-10 Mar-10 Apr-10 May-10 Jun-10 8

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.16 Popes Eye CTD salinity profiles (January – June 2010)

Salinity (psu) 35 35.5 36 36.5 37 37.5 0

Depth (m) Depth 8

Jan-10 Feb-10 Mar-10 Apr-10 May-10 Jun-10 14

The IMOS shipborne data also shows the influence of the Yarra River and Bass Strait as reflected in the lower salinities. The influence of the Yarra River on salinity in the Bay is most evident and extends further into the Bay when catchment inflows are high and consistent as seen in late 2009. During the current reporting period, the influence of the Yarra did not extend as far into the Bay as there were less consistent freshwater inputs (Figure A3.17). Figure A3.17 IMOS shipborne salinity measurements for PPB (August 2008 – July 2009 and September 2009 – June 2010)

Decreases in salinity associated with rainfall also influenced chlorophyll-a concentrations in Hobsons Bay. Data from the NCBMP show increased chlorophyll fluorescence in January, February and March 2010 coinciding with low salinity (Figure A3.18). Figure A3.18 Hobsons Bay surface salinity and chlorophyll-a measurements (December 2009 – June 2010)

38 12

37 10

36 8

35 6 Salinity (psu) Salinity

34 4 (ug/L) Chlorophyll-a

33 2

32 0 14-10-2009 03-12-2009 22-01-2010 13-03-2010 02-05-2010 21-06-2010 10-08-2010

DPI nutrient cycling surface salinity data Date DPI nutrient cycling surface chl-a data

Stratification The Detailed Design states that stratification is deemed to occur where there is a difference of greater than 10 psu in salinity or the temperature differs by more than 0.5°C between surface and bottom waters.26 During this reporting period (January – June 2010) there were a number of instances of temperature stratification, most notably in February (Table A3.4). Table A3.4 Temperature Stratification in PPB (January – June 2010) Month Location Temperature Change Salinity Change Feb-10 Yarra River at Newport 0.97 -1.35 Feb-10 Hobsons Bay 1.19 -0.06 Feb-10 Central Bay 1.86 0.02 Feb-10 PoM DMG 1.81 0.03 Feb-10 Corio Bay 0.68 -0.07 Feb-10 Long Reef 0.80 0.03 Mar-10 Yarra River at Newport 1.66 -5.86 Mar-10 Hobsons Bay 1.08 -0.60 Mar-10 Long Reef 0.86 -0.87 Apr-10 Yarra River at Newport 1.11 -6.57 Apr-10 Hobsons Bay 0.51 -0.54 May-10 Patterson River -0.70 -2.29

26 PoMC 2010. Water Quality – Detailed Design CDP_ENV_MD_023 Rev 5.0 Port of Melbourne Corporation.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Temperature stratification is most common from August to February in low wind conditions when the air temperature exceeds the water temperature.27 At sites close to rivers the temperature stratification was correlated to salinity with fresh water overlaying the seawater. This was most evident at the Yarra River at Newport site in March and April (Figure A3.19). Figure A3.19 Yarra River at Newport stratification (February 2010)

Temperature (oC) 22.4 22.6 22.8 23 23.2 23.4 23.6 23.8 24 0 34.2

1.5 34.8 Depth(m) Salinity (PSU)

3 35.4

Temperature-depth

Salinity-temperature

4.5 36

In March at the Yarra River at Newport and Long Reef sites the increase in salinity also coincided with a decline in DO from the surface to the halocline and then an increase in DO in the lower waters. Chlorophyll fluorescence measurements at these sites also followed the same pattern (Figure A3.20 and Figure A3.21). Figure A3.20 CTD profile of salinity, DO and fluorescence at Yarra River Newport (March 2010)

27 Black and Mourtikas 1992 Literature review of the physics of Port Phillip Bay, Port Phillip Bay Environmental Study Technical Report No.3

Figure A3.21 CTD profile of salinity, DO and fluorescence at Long Reef (March 2010)

Dissolved Oxygen (DO)

Under natural conditions, DO concentrations may vary greatly over a daily (or diurnal) period depending on water temperature, salinity, photosynthetic and microbial activity.28 There were two occasions when the WQBMP DO dropped below 90% at the Yarra River at Newport site in April and May 2010 (Table A3.3). Results from the NCBMP show the variability that can occur in DO readings that is not evident in single samples collected for the WQBMP (Figure A3.22). Figure A3.22 Hobsons Bay surface DO measurements (January – June 2010)

120

110

100

90 Dissolved Oxygen (%sat)Oxygen Dissolved

70 14-10-2009 03-12-2009 22-01-2010 13-03-2010 02-05-2010 21-06-2010 10-08-2010 Date DPI nutrient cycling surface data EPA water quality data (lab) EPA water quality data (CTD)

28 ANZECC 2000. Australian and New Zealand Guidelines for Fresh and Marine Water Quality (2000), Australian and New Zealand Environment Conservation Council

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

In February and April 2010 reduced oxygen concentrations were detected in the centre of PPB. During February the decline in DO at depth corresponded to an increase in chlorophyll fluorescence (Figure A3.23 and Figure A3.24).

Figure A3.23 CTD profile of DO and chlorophyll fluorescence at Central Bay (April 2010)

Figure A3.24 CTD profile of DO and chlorophyll fluorescence at PoM DMG (April 2010)

During April 2010, the reduced oxygen concentrations coincided with colder temperature and higher salinity (Figure A3.25 and Figure A3.26) similar to the same period in 2009.29

Figure A3.25 CTD profile of salinity, temperature and DO at Central Bay (April 2010)

Figure A3.26 CTD profile of salinity, temperature and DO at PoM DMG (April 2010)

29 EPA 2009 Baywide Water Quality Monitoring Program Milestone Report No.4

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Water Clarity - Secchi disc

Secchi disc depth is the measure of water clarity for which SEPP (WoV) objectives are set in Schedule F6. These objectives are applied as control values for water clarity as there are no Shewhart limits available and also no EWMA applicable for these measurements. Water clarity as measured by Secchi disc was generally good across the bay with SEPP (WoV) objectives met at most sites. An improvement in water clarity was seen at the Yarra River at Newport with the SEPP (WoV) objective of greater than 2m met in May and June 2010 (Figure A3.27). Figure A3.27 Water clarity (Secchi depth) at Yarra River at Newport (November 2007– June 2010)

A decline in water clarity was observed at Corio Bay from February to May 2010 (Figure A3.28). Natural and site specific processes including wind, storms, local currents and tides and increased phytoplankton growth can all influence Secchi disc depth measurements. Figure A3.28 Water clarity (Secchi depth) at Corio Bay (November 2007– June 2010)

Water Clarity - Turbidity Turbidity is the measure of water clarity for which SEPP objectives are set in Schedule F7 for the Yarra Port segment of the Yarra River. Turbidity measurements at the Yarra River at Newport site remained below 10 NTU for the last six months, a significant difference when compared to the same period in 2009 (Figure A3.29). The annual median (3.8 NTU) and annual 90th percentile (5.4 NTU) for the last 12 months of monitoring were well below the SEPP objectives of less than 20 NTU and 50 NTU respectively (Table A6.1). Figure A3.29 Yarra River at Newport CTD turbidity profile (January - June 2009; January - June 2010)

Turbidity (NTU) 0 5 10 15 20 25 0

8 Depth (m) Depth 10

14 CTD limit of recording

16 Jan-09 Feb-09 Mar-09 Apr-09 May-09 Jun-09 Jan-10 Feb-10 Mar-10 Apr-10 May-10 Jun-10

Total suspended solids (TSS) The TSS SEPP F7 objectives for Yarra River at Newport were met with the median (6.7 mg/L) and 90th percentile (8.3 mg/L) below the SEPP objectives of less than 25 mg L-1 and 60 mg L1 respectively (Table A6.1).

Light - Photosynthetically active radiation (PAR)

PAR is a measure of light penetration through the water column. The SEPP (WoV) objectives for PAR were met at all sites with the exception of Yarra River at Newport and Sorrento Bank (Appendix 6). At the Yarra River at Newport, high light attenuation is consistent with proximity to freshwater (turbid) inflows and higher chlorophyll-a concentrations, while Sorrento Bank is a very shallow site.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Nutrients

Control limits in the form of Shewhart and EWMA have been derived for nutrients using historic and site specific data to detect changes in water quality outside natural variability in PPB. SEPP (WoV) Schedule F6 excludes nutrient objectives (and default ANZECC values) in recognition of the limited value current ANZECC water quality guidelines for nutrients have in PPB.30 Rather the effects of increased nutrients are assessed through their primary response (increased phytoplankton production) with SEPP (WoV) objectives for chlorophyll-a concentrations. The expected variation in water quality for nutrients in PPB is most effectively expressed via the control limits.

Ammonium

Throughout the current reporting period, concentrations of ammonium have remained relatively steady and below the Shewhart control limits. The exception was an isolated Shewhart exceedence in May 2010 at the PoM DMG (Figure A3.30). EWMA exceedences were again observed at Dromana (Figure A3.31). A small underlying increase was also observed in ammonium EWMA values from January to May 2010 at sites along the east coast (Figure A3.31), central PPB (Figure A3.32) and the Yarra River (Figure A3.33).

Figure A3.30 Ammonium Shewhart control chart for PoM DMG (November 2007 – June 2010)

30 EPA 2002 Port Phillip Bay Water Quality. Long-term Trends in Nutrient Status and Clarity 1984–1999.

Figure A3.31 Ammonium EWMA control chart for Dromana (November 2007 - June 2010)

Figure A3.32 Ammonium EWMA control chart for Central Bay (November 2007 - June 2010)

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.33 Ammonium EWMA control chart for Yarra River at Newport (November 2007 - June 2010)

Nitrate plus Nitrite Concentrations of NOx have remained below Shewhart control limits at all sites for the past six months (Figure A3.34). EWMA exceedences continued at the Yarra River at Newport site (Figure A3.35) following peaks associated with catchment inputs (Figure A3.36). Data from Melbourne Water for the Yarra River also shows the influence of rainfall on nutrient concentrations in the river with a large peak in NOx (and other nutrients) coinciding with the storm event in March (Figure A3.37). Figure A3.34 NOx Shewhart control chart for Central Bay (November 2007 - June 2010)

Figure A3.35 NOx EWMA control chart for Yarra River at Newport (November 2007 - June 2010)

Figure A3.36 River flow and NOx measurements for Yarra River at Newport (May 2006 - June 2010)

6000 300

5000 250

4000 200

3000 150 River flow (ML/day) Concentration (ug/L) Concentration 2000 100

1000 50

0 0 Jul-09 Jul-06 Jan-10 Jan-07 Jun-08 Oct-09 Oct-06 Apr-07 Feb-08 Sep-08 Dec-08 Dec-05 Aug-07 Aug-10 Nov-07 Mar-09 Mar-06 May-10 Date

Mean Daily Flow Jan 06 - April 07 Mean Daily Flow November 07 - June 10 Historical NOx Current NOx

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.37 Melbourne Water and EPA NOx data (January – June 2010)

1000 6000

900

5000 800

700 4000

600

500 3000

400 Riverflow(ML) Concentration (ug/L)Concentration 2000 300

200 1000

100

0 0 1/01/2010 21/01/2010 10/02/2010 2/03/2010 22/03/2010 11/04/2010 1/05/2010 21/05/2010 10/06/2010 30/06/2010 Date

Yarra River at Princes Bridge (MW) Yarra River at Newport (EPA) Fairfield Riverflow

In the south of the bay, small peaks in NOx, corresponding with lower water temperature and salinity, were again observed (Figure A3.38). Seasonal winter peaks of varying magnitude have been previously observed.31 Figure A3.38 NOx Shewhart control chart for Popes Eye (November 2007 - June 2010)

31 EPA 2010 Baywide Water Quality Monitoring Program Milestone Report No.5

Total Nitrogen

Total Nitrogen concentrations over the past six months were below the control limits at all sites except the Yarra River at Newport and Corio Bay. As with NOx, high concentrations of total nitrogen at the Yarra River at Newport site were associated with catchment inputs. This resulted in exceedences of the Shewhart (Figure A3.39) and EWMA control limits at this site (Figure A3.40). Figure A3.39 Total nitrogen Shewhart control chart for Yarra River at Newport (November 2007 - June 2010)

Figure A3.40 Total nitrogen EWMA control chart for Yarra River at Newport (November 2007 - June 2010)

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

The single Shewhart exceedence in February (Figure A3.41) and EWMA exceedence in May at Corio Bay (Figure A3.42) was also influenced by increased rainfall over the catchment.

Figure A3.41 Total nitrogen Shewhart control chart for Corio Bay (November 2007 - June 2010)

Figure A3.42 Total nitrogen EWMA control chart for Corio Bay (November 2007 - June 2010)

Phosphate Phosphate concentrations at all sites, except Dromana, have either remained steady (Figure A3.43 and Figure A3.44) or increased slightly over the past six months (Figure A3.45 and Figure A3.46). Data from the WTP has shown an increase in phosphate and total phosphorous loads over the last six months peaking at the end of May (Figure A3.47). WTP is a significant source of phosphate into PPB (Figure A3.48). The

greatest peaks in phosphate concentrations at Long Reef coincide with the lowest salinities, indicative of WTP (freshwater) discharges (Figure A3.49). Yarra River nutrient data from Melbourne Water show phosphate concentrations are generally lower than those in PPB with no observable peak during the storm event as seen for other nutrients (Figure A3.50). Figure A3.43 Phosphate Shewhart control chart for Corio Bay (November 2007 - June 2010)

Figure A3.44 Phosphate EWMA control chart for Corio Bay (November 2007 - June 2010)

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.45 Phosphate Shewhart control chart for Central Bay (November 2007 - June 2010)

Figure A3.46 Phosphate EWMA control chart for Central Bay (November 2007 - June 2010)

Figure A3.47 WTP nutrient loads (January – June 2010)

8000

6000

4000 Total load (kg/day) load Total

2000

0 01/01/10 21/01/10 10/02/10 02/03/10 22/03/10 11/04/10 01/05/10 21/05/10 10/06/10 30/06/10 Date WTP PO4 WTP TP WTP NH3 WTP TN WTP NOx

Figure A3.48 WTP phosphate loads (May 2008 – June 2010)

4500

4000

3500

3000

2500

2000 PO4 load (kg/day) load PO4

1500

1000

500

0 Feb-08 Jun-08 Sep-08 Dec-08 Mar-09 Jul-09 Oct-09 Jan-10 May-10 Aug-10 Date

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.49 Long Reef salinity and phosphate measurements (November 2007 – June 2010)

450

400

350

300

250

200

150 PO4 Concentration (ug/L) Concentration PO4

100

0 35.5 36 36.5 37 37.5 38 38.5 Salinity (PSU)

Figure A3.50 Melbourne Water and EPA phosphate water quality data (January – June 2010)

100 6000

90 5000 80

70 4000 60

50 3000

40 Riverflow (ML) Concentration (ug/L) Concentration 2000 30

20 1000

0 0 1/01/2010 21/01/2010 10/02/2010 2/03/2010 22/03/2010 11/04/2010 1/05/2010 21/05/2010 10/06/2010 30/06/2010 Date

Yarra River at Princes Bridge (MW) Yarra River at Newport (EPA) Fairfield Riverflow

The general decline in phosphate concentrations across the Bay observed during previous reporting periods is only continuing at Dromana (Figure A3.51 and

Figure A3.52). Phosphate concentrations in the south of PPB appear to be diluted by ocean water with the lowest concentrations correlated to low salinities (Figure A3.53). Figure A3.51 Phosphate Shewhart control chart for Dromana (November 2007 - June 2010)

Figure A3.52 Phosphate EWMA control chart for Dromana (November 2007 - June 2010)

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.53 PPB salinity and phosphate concentrations (November 2007 - June 2010)

100

Central Bay 60 Dromana Corio Bay PoM DMG MGS 40 Sorrento Phosphate (ug/L) Popes Eye Dilution Evaporation

0 35 36 37 38 39 Salinity (psu)

Total Phosphorus

The concentrations of total phosphorus are below the Shewhart and EWMA control limits at all sites. Similar to phosphate, total phosphorus concentrations at all sites except Dromana have remained steady (Figure A3.54 and Figure A3.55) or increased slightly (Figure A3.56 and Figure A3.57) over the past six months. Dromana continues to show a decline in total phosphorus concentrations (Figure A3.58 and Figure A3.59). External data from Melbourne Water shows there was a high concentration of total phosphorus in the Yarra River following the storm event in March (Figure A3.60) and an increase over the last six months from the WTP (Figure A3.47). Figure A3.54 Total Phosphorus Shewhart control chart for Hobsons Bay (November 2007 - June 2010)

Figure A3.55 Total Phosphorus EWMA control chart for Hobsons Bay (November 2007 - June 2010)

Figure A3.56 Total Phosphorus Shewhart control chart for PoM DMG (November 2007 - June 2010)

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.57 Total Phosphorus EWMA control chart for PoM DMG (November 2007 - June 2010)

Figure A3.58 Total Phosphorus Shewhart control chart for Dromana (November 2007 - June 2010)

Figure A3.59 Total Phosphorus EWMA control chart for Dromana (November 2007 - June 2010)

Figure A3.60 Melbourne Water and EPA total phosphorus water quality data (January – June 2010)

700 6000

600 5000

500 4000

400

3000

300 Riverflow(ML) Concentration (ug/L) 2000 200

1000 100

0 0 1/01/2010 21/01/2010 10/02/2010 2/03/2010 22/03/2010 11/04/2010 1/05/2010 21/05/2010 10/06/2010 30/06/2010 Date

Yarra River at Princes Bridge (MW) Yarra River at Newport (EPA) Fairfield Riverflow

Silicate

There are no control limits or SEPP (WoV) objectives for silicate. Highest silicate concentrations were reported at the Yarra River at Newport site (Figure A3.61), with smaller peaks also observed in early 2010 at Corio Bay (Figure A3.62), Patterson River (Figure A3.63) and Popes Eye (Figure A3.64).

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.61 Silicate control chart for Yarra River at Newport (November 2007 - June 2010)

Figure A3.62 Silicate control chart for Corio Bay (November 2007 - June 2010)

Figure A3.63 Silicate control chart for Patterson River (November 2007 - June 2010)

Figure A3.64 Silicate control chart for Popes Eye (November 2007 - June 2010)

Phytoplankton and Algal Pigments Phytoplankton activity is measured through cell counts, chlorophyll-a measurements and in-situ chlorophyll fluorescence. Total phytoplankton cell counts in the past six months have declined from the high numbers seen at some sites in November and December 2009 (Figure A3.65). Phytoplankton cell counts did remain above bloom levels (nominally >1,400,000 cells/L)32 at the Yarra River at Newport and Hobsons Bay sites in

32 Hale 2006 Supplementary Environment Effects Statement, Head Technical Report: Nutrient Cycling- Appendix 1 Phytoplankton Blooms

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

January and February 2010 and Corio Bay in March 2010. Phytoplankton blooms are a natural occurrence within PPB with previous studies finding higher concentrations of phytoplankton in warmer months with peaks in late summer/ early autumn.33 Early 2010 was the first occasion during the WQBMP that potentially harmful phytoplankton were detected above the Victorian Shellfish Operations Manual (VSOM) action levels. The potentially harmful diatoms, Pseudo-nitzschia species, made up 35% and 87% of the phytoplankton community at the Yarra River at Newport and Hobsons Bay sites, respectively in January. Pseudo-nitzschia species have occurred previously in PPB with large blooms detected in 1988, 1991/92, 1993/94 and 1996 (Figure A3.66).35 The largest bloom of Pseudo-nitzschia species was recorded in 1991/92 with the bloom extending across many areas of PPB (Figure A3.67). 35 The highest cell counts for this species were measured at St Kilda in December 1991 with a peak of approximately 4,250,000 cells/L and Hobsons Bay in February 2010 with a peak of 3,650,000 cells/L (Figure A3.68). 34 Following the presence of Pseudo-nitzschia spp. in January, the toxic dinoflagellate, Alexandrium catenella, first identified in PPB in 1986, was detected at the Yarra River at Newport site in February 2010. A. catenella blooms have only been recorded in Hobsons Bay during summer (December to mid-April), and cysts are known to be abundant near the Yarra mouth.35 Another potentially harmful dinoflagellate, Karlodinium species (not reported in Progress reports), was detected above VSOM levels in March and April 2010 in Corio Bay. Pseudo-nitzschia species were again detected above VSOM levels in Corio Bay in April 2010 making up 40% of the phytoplankton community. Figure A3.65 Total phytoplankton cell numbers across PPB (February 2008 – June 2010)

12000000

10000000

8000000

6000000

4000000 Total Phytoplankton (cells/L) Total Phytoplankton

2000000

0 Jul-09 Jul-08 Jan-10 Jan-09 Jun-09 Jun-08 Oct-09 Oct-08 Apr-10 Apr-09 Apr-08 Feb-10 Sep-09 Feb-09 Sep-08 Feb-08 Dec-09 Dec-08 Aug-09 Aug-08 Nov-09 Nov-08 Mar-10 Mar-09 Mar-08 May-10 May-09 May-08 Date

Yarra River at Newport Hobsons Bay Central PoM DMG Corio Bay Long Reef Patterson River Dromana Middle Ground Shelf Sorrento Popes Eye

33 Elias et al. 2004 Port Philip Bay Channel Deepening Project Environmental Effects Statement – Marine Ecology Specialist Studies, Volume 8 Plankton and Nekton studies. 34 Longmore 2010 DPI phytoplankton data 1987 - 1996 35 Arnott et al. 1995 Phytoplankton composition, distribution and abundance in Port Phillip Bay from March 1990 to February 1995.

Figure A3.66 Average Pseudo-nitzschia species cell counts from PPB (1998 – 1996; 2008 -2010)

1600000

1400000 CDP - 2010 CDP - 2009 CDP - 2008 1200000 1996 1995 1000000 1994 1993 1992 800000 1991 Total Pseudo Pseudo Total

nitzschia (cells/L)nitzschia 1990 600000 1989 1988 400000

200000 1989 1991 1993 0 1995 Jan Feb CDP - 2008 Mar Apr May Jun Jul Aug CDP - 2010 Sep Oct Nov Dec

Figure A3.67 Pseudo-nitzschia species cell counts across PPB (1991)

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.68 Pseudo-nitzschia species cell counts in PPB (1988-1996; 2008-2010)

4500000

4000000

3500000

3000000

2500000

2000000

Phytoplankton (cells/L) Phytoplankton 1500000

1000000

500000

0 1988 1989 1990 1991 1992 1993 1994 1995 1996 2008 2009 2010 Date

Beaumaris St Kilda Dromana Balcolmbe Bay Williamstown Popes Eye Patterson River Hobsons Bay

Phytoplankton growth and productivity are primarily influenced by temperature, light and nutrients with salinity stratification potentially initiating blooms.36.

36 Wood and Beardall 1992 Phytoplankton ecology of Port Phillip Bay Port Phillip Bay Environmental Study

Figure A3.69 and Figure A3.70 provide a general view of the spatial variation seen in temperature, salinity, silicate, phosphate, dissolved inorganic nitrogen (DIN), chlorophyll-a and phytoplankton in Hobsons and Corio Bay, the two most productive areas during the current reporting period, using data interpolated with the Spline method.37

37 The interpolation of data presented here is intended to give a general impression of spatial variation across the bay. It is developed from the sampling data collected at the 11 WQBMP sites over a number of days each month and does not account for minor temporal changes caused by environmental factors.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.69 Hobsons Bay interpolated water quality data (January – June 2010)

Figure A3.70 Corio Bay interpolated water quality data (January – June 2010)

The phytoplankton cell counts from the above two sites once again did not correspond to the chlorophyll- a data. Significant shifts in phytoplankton community composition may explain the disparity in results. Figure A3.71 show the change in species composition at these two sites from January – March 2010 as an example.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.71 Yarra River at Newport and Corio Bay phytoplankton species composition (January – March 2010)

Yarra River at Newport January 2010 Corio Bay January 2010

Diatoms Diatoms (% of total Phytoplankton) (% of total Phytoplankton) Other Diatoms 7% Pseudo-nitzschia Chaetoceros spp. 6% delicatissima group Cyl. Closterium 6% Cryptophytes Diatoms 34.8% 15% Diatoms Cryptophytes 85% 64% 9.9% Skeletonema Skeletonema Dinoflagellates 45% 43.7% 15%

Yarra River at Newport February 2010 Corio Bay February 2010

Diatoms Diatoms (% of total Phytoplankton) (% of total Phytoplankton) Cryptophytes Chaetoceros spp . 11.3% 34% Other Diatoms 8%

Cryptophytes Diatoms Diatoms 15.5% 77% Skeletonema 19% 57.2% Cyl. Closterium 8% Dinoflagellates 33%

Yarra River at Newport March 2010 Corio Bay March 2010

Diatoms Diatoms (% of total Phytoplankton) (% of total Phytoplankton)

Other Diatoms 15% Chaetoceros spp . 27.4% Chaetoceros spp. 19% Cryptophytes Diatoms Diatoms 35% 62% Dinoflagellates 87% 8% Skeletonema Cyl. Closterium 50% 25.7%

The chlorophyll-a concentrations from the WQBMP and chlorophyll fluorescence from the IMOS shipborne data also indicate continued phytoplankton activity throughout the Bay (Figure A3.72). The SEPP (WoV) annual 90th percentile objectives were exceeded at Yarra River at Newport, Corio Bay and Patterson River (Appendix 6). High chlorophyll-a concentrations and EWMA exceedences continued at the Yarra River at Newport (Figure A3.73 and Figure A3.74) and elevated chlorophyll-a concentrations and EWMA exceedences were also reported at Corio Bay for each of the last five months (Figure A3.75 and Figure A3.76). Figure A3.72 IMOS shipborne in-situ chlorophyll fluorescence measurements for PPB (August 2008 – July 2009 and September 2009 – June2010)

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.73 Chlorophyll a control chart for Yarra River at Newport (November 2007 - June 2010)

Figure A3.74 Chlorophyll a EWMA control chart for Yarra River at Newport (November 2007 - June 2010)

Figure A3.75 Chlorophyll a control chart for Corio Bay (November 2007 - June 2010)

Figure A3.76 Chlorophyll a EWMA control chart for Corio Bay (November 2007 - June 2010)

The seasonal winter peaks in chlorophyll-a in the south of PPB also resulted in EWMA exceedences at Sorrento Bank (Figure A3.77) and MGS in June.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.77 Chlorophyll a EWMA control chart for Sorrento Bank (November 2007 - June 2010)

Metals Most of the metal samples collected during the last six months were below the limit of reporting (LOR) and control limits. There was only one reported metal exceedence, total chromium at the Yarra River at Newport in March, following the storm event. Peaks in other metal concentrations associated with the storm event in March 2010 reported by the Melbourne Water (Figure A3.78) and the Beach monitoring programs (Figure A3.79) were not reflected in the WQBMP data. Figure A3.78 Yarra River Melbourne Water metals data (January – June 2010)

70 6000

60 5000

50 4000

3000

30 Riverflow(ML/day) Concentration (ug/L) Concentration 2000 20

1000 10

0 0 1/01/2010 21/01/2010 10/02/2010 2/03/2010 22/03/2010 11/04/2010 1/05/2010 21/05/2010 10/06/2010 30/06/2010 Date

Cr As Cu Pb Zn Ni Cd Fairfield Riverflow

Figure A3.79 St Kilda Beach monitoring metals data (January – June 2010)

20 6000 19 18 17 5000 16 15 14 4000 13 12 11 10 3000 9 8 Riverflow(ML/day) Concentration(ug/L) 7 2000 6 5 4 1000 3 2 1 0 0 1/01/2010 21/01/2010 10/02/2010 2/03/2010 22/03/2010 11/04/2010 1/05/2010 21/05/2010 10/06/2010 30/06/2010 Date

As Cd Cr Cu Pb Hg Ni Zn Yarra River at Fairfield Riverflow

Summary statistics for metals have been calculated for comparison against SEPP objectives. Regionally specific SEPP (WoV) objectives apply to total metals. Where there is no regionally specific objective in SEPP (WoV), the SEPP (ANZECC) objective is applied to dissolved metals (Appendix 6). Summary statistics are calculated using the last 12 months of data (July 2009 – June 2010) and include the mean, median, 90th percentile, minimum and maximum value. SEPP (WoV) objectives for metals are based on maximum values.

Arsenic

Arsenic concentrations during the current reporting period were all below the Shewhart and EWMA control limits (where available). Concentrations generally remained steady (Figure A3.80 and Figure A3.85) or showed a small increase since the previous reporting period (Figure A3.86 and Figure A3.83). Summary statistics based on the last 12 months of data show the SEPP (WoV) F6 objective of less than 3µgL/L was not met at Corio Bay (Appendix 6) with a maximum value of 3.2 µg/L reported in March 2010. The SEPP (WoV) objective for arsenic in PPB is based on background measurements, rather than on toxicity and there is currently no evidence that exceeding the SEPP (WoV) objective by a small margin constitutes a risk to marine biota.38

38 Gibbs et al 2007 Port of Melbourne Corporation Channel Deepening Project Baseline Water Quality Monitoring 2006- 2007

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.80 Arsenic control chart for Dromana (November 2007 - June 2010)

Figure A3.81 Arsenic EWMA control chart for Dromana (November 2007 - June 2010)

Figure A3.82 Arsenic control chart for Central Bay (November 2007 - June 2010)

Figure A3.83 Arsenic EWMA control chart for Central Bay (November 2007 - June 2010)

Cadmium

All samples in the current reporting period were below the LOR (0.2 µg/L) and within both control limits and SEPP (WoV) objectives. Summary statistics based on the last 12 months of data show the SEPP (WoV) F6 objective of less than 0.15µg/L (which is below the LOR) was met at all sites (Appendix 6).

Chromium

There was only one recorded chromium exceedence during the reporting period with total chromium exceeding the Shewhart control limit at the Yarra River at Newport in March (Figure A3.84). Summary

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

statistics based on the last 12 months of data show the SEPP (WoV) F6 objective of less than 5.0 µg/L was met at all sites (Appendix 6). Figure A3.84 Total chromium control chart for Yarra River at Newport (November 2007 - June 2010)

Copper

The majority of samples in the current reporting period were below the LOR (1.0µg/L) and within both control limits and SEPP (ANZECC) objectives. Dromana and the Yarra River at Newport (Figure A3.85 and Figure A3.86) were the only sites where copper concentrations were greater than or equal to the LOR. Summary statistics based on the last 12 months of data show the SEPP (ANZECC) F6 objective was met at all sites (Appendix 6). Figure A3.85 Total copper Shewhart control chart for Yarra River at Newport (November 2007 - June 2010)

Figure A3.86 Dissolved copper control chart for Yarra River at Newport (November 2007 - June 2010)

Lead

The majority of samples in the current reporting period were below the LOR (0.2 µg/L) and within both control limits and SEPP (ANZECC) objectives. The Yarra River at Newport was the only site that consistently reported values above the LOR for total lead (Figure A3.87). Dissolved lead was generally below the LOR (Figure A3.88). Summary statistics based on the last 12 months of data show the SEPP (ANZECC) F6 objectives were met at all sites (Appendix 6). Figure A3.87 Total lead Shewhart control chart for Yarra River at Newport (November 2007 - June 2010)

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Figure A3.88 Dissolved lead control chart for Yarra River at Newport (November 2007 - June 2010)

Mercury

All mercury samples were below the LOR and control limits throughout the current reporting period. Summary statistics based on the last 12 months of data show the SEPP (WoV) F7 and SEPP (ANZECC) F6 objectives were not met at a number of sites due to mercury results in November 2009 reported at concentrations equal to the LOR (Appendix 6).

Nickel

All nickel samples in the current reporting period were below the Shewhart control limits. Summary statistics based on the last 12 months of data show the SEPP (ANZECC) F6 objectives were met at all sites (Appendix 6).

Zinc

The majority of samples in the current reporting period were below the LOR (5.0 µg/L) and within derived control limits. Summary statistics based on the last 12 months of data show the SEPP (WoV) objectives were not met at Corio Bay and the Yarra River at Newport due to high concentrations recorded during the previous reporting period (Appendix 6).

TBT

All TBT samples, from the Yarra River at Newport and Hobsons Bay sites, were below the LOR and/or within both the Shewhart control limits and the SEPP (ANZECC) objectives throughout the reporting period (Appendix 6)

100

APPENDIX 4 - QA/QC DATA AND DISCUSSION Laboratory QA/QC The respective laboratories for this monitoring program have reported their quality control for the sample batches covered by this report to be within acceptable limits.

Phytoplankton Analysis

Microalgal Services laboratory protocols and procedures aim to comply with AS ISO/IEC 17025-2005 (General Requirements for the competence of testing and calibration laboratories). Equipment is calibrated to NATA traceable standards and method validation has been undertaken.

Nutrient Analysis Department of Primary Industries (DPI) Queenscliff laboratory’s QA/QC program includes: • Laboratory blanks, analysed with each batch of samples; • Laboratory spikes, analysed with each batch of samples; • Spike recovery analysed periodically; • Algorithm checks are carried out periodically to assure the accuracy of nutrient calculations; and • All samples analysed in duplicate.

Metals Analysis

Ecowise (now a subsidiary of Australian Laboratory Services (ALS)) employs a QAQC program as follows:

• Method Blanks, analysed with each batch of samples; • Laboratory Duplicates, analysed with each batch of samples;

• Laboratory Control Samples (LCS), analysed with each batch of samples; and

• Matrix Spikes (MS), analysed with each batch of samples.

Laboratory comparison on filtered and unfiltered nitrates

The current WQBMP measures filtered inorganic nutrients whereas historically, inorganic nutrients were measured using unfiltered samples. This inconsistency prompted an investigation as detailed in EPA (2009)39. Filtered and unfiltered samples for nitrates (nitrate and nitrite) were analysed due to the potential contamination of filtered samples in April – June 2009. A further comparison using new filters was completed from January – June 2010.

The first comparison in 2009 found that for 98% of the NOX samples, the filtered result was greater than the unfiltered result. This indicated that the control limits based on unfiltered samples may not be adequate as there was the potential for false exceedences. In contrast, the second comparison undertaken in 2010 found that for 57% of the NOX samples, the filtered result was greater than the unfiltered result. Since implementation of the new filters, the difference between the filtered and unfiltered samples has been within the measurement of uncertainty provided by the laboratory and has not caused any control limits to be exceeded. The change in filters has decreased the risk of contamination and therefore the potential for false exceedences. The control limits remain conservative and are fit for purpose.

39 EPA 2009 Filenote Comparison of filtered and unfiltered nutrient data

101

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Sample blanks and replicates Field sampling quality control measures include the collection of field blanks and replicates to test for contamination and laboratory precision.

Field Sample blanks

The majority of field blanks analysed by the laboratories have come back with values less than the LOR. The only exception was: • A positive result for filtered chromium (0.8µg/L) was reported in the Day 3 field blank in May 2010. Re-analysis of the sample resulted in a reported value of <0.5µg/L. When applying the measurement uncertainty (MU) (0.644 µg/L) to the original sample result, the two values are consistent and were accepted as valid.40

Field replicate samples

Most metal replicate samples for the period January – June 2010 were found to be in agreement with the original value. There were two occasions, in January and March 2010, when internal QAQC investigations of the replicate data found that the samples may have been contaminated and no results were reported. • January 2010: The replicate filtered and unfiltered value for lead at Hobsons Bay was outside of the MU of the original sample. The reported original unfiltered result for lead (1.2 µg/L) exceeded the Shewhart control limit of 0.95 µg/L while the replicate value was reported as <0.2 µg/L. The re- analysed results were consistent and the data was rejected.41 • March 2010: The laboratory automatically re-analysed the samples for Central Bay and the Northern Replicate (PoM DMG) when filtered results for chromium, nickel and zinc were higher than the unfiltered results. Internal QAQC procedures identified the following issues: 1. The original filtered zinc result for PoM DMG was not consistent with the Northern Replicate collected at the same site indicating that the zinc was not at the sample site but from an external source. 2. The filtered zinc results for Central Bay and the Northern Replicate (PoM DMG) were considerably greater (and outside of MU) than the unfiltered. 3. The filtered chromium result for Central Bay was outside of the measurement uncertainty (MU) of the unfiltered result. The source of the contamination of the samples is unknown. No results were reported in March 2010 for filtered chromium, nickel and zinc data for Central Bay. The Northern Replicate results for these parameters were also considered invalid.42

Nutrient replicate samples for the period January – June 2010 were also generally found to be in agreement with the original value. The exceptions were: • The Sorrento Bank particulate nitrogen replicate result was outside of the MU of the original result in March 2010. As particulate nitrogen is not reported and the result was below the LOR the data was accepted.43

40 EPA 2010 May 2010 QAQC Report 41 EPA 2010 January 2010 QAQC Report 42 EPA 2010 March 2010 QAQC Report (Ecowise)

102

• The Northern Replicate (Yarra River at Newport) results for carotenoid, chlorophyll-b and phaeopigments and Southern Replicate (Popes Eye) phaeopigment result were not within 10% or the MU of the original results. All results, except carotenoid which is not reported, were accepted as valid based on expert advice from the laboratory.44

Field QA/QC

Comparability of CTD and laboratory results

A small number of discrepancies were found between the CTD and laboratory results. It is expected that differences in results will arise due to the different methodology used in collecting the samples and the time of the analysis. Further factors that may also cause discrepancies include turbulence off the hull, differences in sampling times and differences in collection point of the sample.

Calibration of the CTD

The regular CTD used for water quality monitoring was sent to America for an annual manufacturer’s calibration following the February 2010 sampling.

Use of back-up CTD in March, April and May 2010

A back-up CTD was used to collect in-situ data for the water quality monitoring program in March, April and May 2010 while the regular CTD was undergoing annual calibration. A scalar (spherical) PAR sensor rather than the usual planar (flat) sensor was used for recording PAR during these months. The use of the spherical sensor allows light to be captured from all directions resulting in higher PAR readings. The PAR data, while not directly comparable, can be converted to attenuation (assuming R2 >0.8) allowing for assessment against the SEPP (WoV) F6 90th percentile objectives (Appendix 6).

Comparability of regular and back-up CTD

An inter-comparison of the two CTDs used for the Water Quality Monitoring Program was undertaken during the February 2010 sampling event. The two CTDs were lowered through the water column side by side at each site by different operators. Overall the two CTDs showed good comparability for most parameters. Differences between the CTDs were observed for turbidity, fluorescence and dissolved oxygen at the Yarra River at Newport site. The Yarra River at Newport site is in the Yarra River estuary, which can be affected by freshwater inflows, tides and shipping, creating large amounts of variability over small distances.

43 EPA 2010 March 2010 QAQC Report (DPI) 44 EPA 2010 June 2010 QAQC Report

103

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

APPENDIX 5 - RESULTS OUTSIDE OF NATURAL/EXPECTED VARIABILITY

As outlined in the Detailed Design (Decision Framework for Management) an assessment was undertaken of results flagged as outside of natural/expected variability. This is reported monthly in Assessment Reports.45,46 In summary, the assessment undertakes the following basic steps:

1. Are the results outside natural/expected variability? This is a two part question: a. Are results outside of expectations based on our understanding of ‘natural’ historical background conditions in the Bay? - This is determined by assessing results against control limits. If the results exceed control limits then they are deemed to be ‘outside of natural variability’. b. Are such results outside of our expectations based on the predicted effects of the CDP, as defined in the Supplementary Environment Effects Statement (SEES) – This assessment is based on expert opinion. 2. If results are deemed to be ‘outside expected variability’, then a decision is made to determine if these changes are significant to the environment. This will consider issues such as: • The accuracy of the results • The magnitude of deviation from expectations

• The temporal and spatial extent of changes

• The biological significance of changes. 3. Under the Decision Framework for Management, if an assessment concludes that results are of significance to the environment then further risk-based investigations are initiated to identify flow on effects to the ecosystem, the causal factor/s and any required management measures.

Assessment Multiple lines of evidence are considered to assess whether the results are outside of expected variability. All results up to June 2010 have been reviewed by the EPA and PoMC with the identification of the following issues and outcomes summarised in Table A5.1. In all instances, the assessments concluded that the water quality results identified to be outside of expected variability are not of significance to the broader bay environment.

45 PoMC 2010a, b, c, d, Assessment of results outside of expected variability, Progress Report #25-#28 46 EPA 2010a, b, Assessment of results outside of expected variability, Progress Report #29 and #30

104

Table A5.1 PoMC/EPA Assessment (January – June 2010)

PARAMETER SITES EXCEEDENCE TYPE DATES ASSESSMENT OUTCOME Sustained exceedences of ammonium EWMA are considered to be associated with a stepwise increase in Dromana EWMA March - June 2010 concentrations from the 1990's to now and the relatively low control limit at this site. Ammonium The raw result is outside the (limited) historical data range. When compared to the large historical dataset PoM DMG Shewhart May 2010 from the neighbouring Central Bay site, the concentration is within historical limits. The EWMA exceedences are a result of elevated raw values associated with increased catchment inputs. The limited historical dataset was collected during a period of Nitrate plus Nitrite Yarra River at EWMA January - June 2010 lower rainfall and is therefore unlikely to represent (NOx) Newport nutrient conditions in the Yarra River during periods of increased rainfall. Raw results from prior months can have a sustained influence on EWMA values. As above for NOx the EWMA exceedences are a result of elevated raw values associated with increased catchment inputs. The limited historical dataset was collected during Yarra River at EWMA January - June 2010 a period of lower rainfall and is therefore unlikely to Newport represent nutrient conditions in the Yarra River during periods of increased rainfall. Raw values can have a sustained influence on EWMA values. Total Nitrogen This marginal exceedence is likely due to increased (TN) rainfall over the catchment areas since late 2009, leading Shewhart February 2010 to increases in surface runoff and nutrient input into PPB. A similar trend in elevated TN corresponding with Corio Bay elevated rainfall was seen at the same time in 2008/09. This is the first EWMA exceedence at this site and is EWMA May 2010 marginally above the control limit. The raw result is within the historical range.

105

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

PARAMETER SITES EXCEEDENCE TYPE DATES ASSESSMENT OUTCOME EWMA exceedences were localised with the raw results either within the historical range for this site or neighbouring Hobsons Bay. The exceedences from Yarra River at January - March were most likely a response to increased January - June 2010 Newport catchment inputs from increased rainfall, while the continued exceedences from April - June were most likely a result of the sustained influence of raw results on the EWMA calculation.

Chlorophyll a EWMA Chlorophyll a concentrations were localised and within or Corio Bay February - June 2010 marginally outside the historical range.

Middle Ground Although these results were outside the historical range, Shelf these sites are informed by a small historical dataset that does not adequately characterise chlorophyll a June 2010 conditions. The conditions were localised and did not Sorrento Bank extend to the neighbouring sites, Popes Eye and Dromana.

Yarra River at These results are within the varying conditions that are Dissolved Oxygen SEPP April - May 2010 Newport observed in the Yarra River. The SEPP exceedences are a reflection of the limited historical data range available for comparison and Yarra River at increased rainfall and river flows during this period. January - April 2010 Newport When compared to the large historical dataset from the neighbouring Hobsons Bay site, the current Yarra River values are within historical limits. Secchi depth SEPP Hobsons Bay Reduced water clarity may have been due of poor January 2010 weather conditions in the days prior to sampling. Long Reef This exceedence is marginal and within the range Corio Bay May 2010 previously observed at this site. This is a marginal exceedence that is within the historical Yarra River at Total Chromium Shewhart March 2010 range. The dissolved (bio-available) fraction was below Newport the ANZECC limit.

106

PARAMETER SITES EXCEEDENCE TYPE DATES ASSESSMENT OUTCOME Yarra River at These elevated levels are unlikely to be of significance to Newport the longer-term heath of PPB. These species are known January 2010 Pseudo-nitzschia to occur in PPB and elevated results have been reported Hobsons Bay VSOM spp previously. Furthermore, the Yarra River and Hobsons Bay are not aquaculture areas. The species of Pseudo- Corio Bay April 2010 nitzschia detected in Corio Bay were non-toxic and so it is Alexandrium Yarra River at unlikely that the aquaculture activities in this area would VSOM February 2010 catenella Newport be affected.

107

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

APPENDIX 6. - SUMMARY STATISTICS (JULY 2009 – JUNE 2010)

Note: SEPP (WoV) Schedule F6/F7 exceedences are highlighted in blue.

Table A6.1 Yarra River at Newport summary statistics – Schedule F7 Yarra Port Segment Objectives

Dissolved Dissolved Suspended Suspended Oxygen Oxygen Salinity Temperature Turbidity Turbidity Solids Solids

SEPP SEPP SEPP objective objective objective %sat %sat mg/L deg C NTU NTU mg/L mg/L Mean 96 30.8 17.3 3.8 6.3 Median 96 31.5 17.8 3.8 <20 6.7 <25 90th percentile 101 34.5 23.3 5.4 <50 8.3 <60 Minimum 86 >60 25.0 11.3 2.1 2.5 Maximum 116 34.8 24.3 6.9 10.6 N 12 12 12 12 12

Dissolved Dissolved Dissolved Dissolved Dissolved Dissolved Dissolved Total Arsenic Chromium Zinc Cadmium Copper Nickel Lead Mercury

SEPP objective µµµg/L <13 <1 <8 <0.2 <1.3 <11 <3.4 <0.05 Mean 2.0 Median 2.0 <0.5 <5 <0.2 <1 0.8 <0.2 <0.1 90th percentile 2.4 <0.5 10 <0.2 1 0.9 <0.2 <0.1 Minimum 1.4 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.4 <0.5 17 <0.2 1 1.0 0.3 0.1 N 12 12 12 12 12 12 12 12

108

Table A6.2 Yarra River at Newport summary statistics – Schedule F6 Hobsons Segment objectives

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 96 30.8 17.3 1.5 3.52 0.76 Median 96 31.5 17.8 1.3 2.10 2.5 0.64 90th percentile 101 34.5 23.3 2.5 8.09 4.0 1.16 0.50 Minimum 86 >90 25.0 11.3 0.6 >2 0.70 0.33 Maximum 116 34.8 24.3 2.7 8.87 1.72 N 12 12 12 12 12 12

Total Total Dissolved Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury Tributyl Tin

SEPP objective µµµg/L <3 <5 <10 <5.5 <1.3 <70 <4.4 <0.4 <0.006 Mean 2.1 Median 2.1 <0.5 <5 <0.2 <1 0.8 <0.2 <0.1 <0.002 90th percentile 2.5 0.7 14 <0.2 1 0.9 <0.2 <0.1 <0.002 Minimum 1.5 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 <0.002 Maximum 2.6 0.7 20 <0.2 1 1.0 0.3 0.1 <0.002 N 12 12 12 12 12 12 12 12 12

109

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Table A6.3 Hobsons Bay summary statistics

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 99 36.3 17.0 3.2 1.86 0.38 Median 97 36.4 16.6 3.3 1.88 2.5 0.33 90th percentile 107 36.9 21.9 4.3 2.95 4.0 0.43 0.50 Minimum 94 >90 34.9 11.1 1.1 >2 0.57 0.22 Maximum 109 37.1 24.1 4.7 3.64 0.81 N 12 12 12 12 12 12

Total Total Dissolved Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury Tributyl Tin SEPP objective µµµg/L <3 <5 <10 <5.5 <1.3 <70 <4.4 <0.4 <0.006 Mean 2.3 Median 2.4 <0.5 <5 <0.2 <1 0.6 <0.2 <0.1 <0.002 90th percentile 2.7 0.5 <5 <0.2 <1 0.6 0.3 <0.1 <0.002 Minimum 1.7 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 <0.002 Maximum 2.7 1.1 <5 <0.2 <1 0.7 1.2 0.1 <0.002 N 12 12 12 12 12 12 12 12 12

110

Table A6.4 Corio Bay summary statistics

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 103 37.8 16.7 1.44 0.36 Median 101 37.8 16.1 1.03 1.5 0.36 90th percentile 115 38.2 22.8 3.35 2.5 0.44 0.45 Minimum 91 >90 37.4 10.1 2.9 >3 0.63 0.22 Maximum 118 38.3 24.1 >6.4 3.50 0.53 N 12 12 12 12 12 12

Total Total Dissolved Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury SEPP objective µµµg/L <3 <5 <5 <5.5 <1.3 <70 <4.4 <0.4 Mean 2.6 0.7 Median 2.6 <0.5 <5 <0.2 <1 0.7 <0.2 <0.1 90th percentile 2.9 <0.5 <5 <0.2 <1 0.8 0.3 <0.1 Minimum 1.8 <0.5 <5 <0.2 <1 0.5 <0.2 <0.1 Maximum 3.2 <0.5 15 <0.2 1 0.8 0.3 0.1 N 12 12 12 12 12 12 12 12

111

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Table A6.5 Long Reef summary statistics

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 101 37.1 16.8 1.35 0.33 Median 98 37.2 16.2 1.09 2.5 0.32 90th percentile 107 37.5 22.3 1.46 4.0 0.41 0.45 Minimum 92 >90 36.6 9.8 2.7 >3 0.60 0.24 Maximum 121 37.7 24.4 >5.9 4.92 0.43 N 12 12 12 12 12 12

Total Total Dissolved Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury SEPP objective µµµg/L <3 <5 <5 <5.5 <1.3 <70 <4.4 <0.4 Mean 2.4 Median 2.5 <0.5 <5 <0.2 <1 0.6 <0.2 <0.1 90th percentile 2.8 0.7 <5 <0.2 <1 0.8 <0.2 <0.1 Minimum 1.8 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.8 1.0 <5 <0.2 <1 0.9 0.2 0.1 N 12 12 12 12 12 12 12 12

112

Table A6.6 Central Bay summary statistics

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 97 37.0 16.7 9.3 0.69 0.16 Median 97 37.1 17.2 9.3 0.67 1.0 0.17 90th percentile 99 >90 37.3 21.3 11.6 1.15 2.0 0.24 0.35 Minimum 93 >90 36.5 10.8 5.8 >4 0.25 0.09 Maximum 102 37.3 22.9 13.0 1.26 0.24 N 12 12 12 12 12 12

Total Total Total Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury SEPP objective µµµg/L <3 <5 <5 <0.15 <0.3 <7 <2.2 <0.1 Mean 2.3 Median 2.3 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 90th percentile 2.7 <0.5 <5 <0.2 <1 0.5 <0.2 <0.1 Minimum 1.8 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.7 <0.5 <5 <0.2 <1 0.6 <0.2 0.1 N 12 12 12 12 12 11 12 12

113

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Table A6.7 POM DMG summary statistics

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 98 37.0 16.7 8.2 0.76 0.18 Median 97 37.0 16.8 7.8 0.72 1.0 0.18 90th percentile 101 >90 37.3 21.5 12.1 1.27 2.0 0.22 0.35 Minimum 93 >90 36.5 10.6 5.6 >4 0.26 0.09 Maximum 107 37.4 22.8 12.6 1.29 0.29 N 12 12 12 12 12 11

Total Total Total Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury SEPP objective µµµg/L <3 <5 <5 <0.15 <0.3 <7 <2.2 <0.1 Mean 2.3 Median 2.3 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 90th percentile 2.7 <0.5 <5 <0.2 <1 0.6 <0.2 <0.1 Minimum 1.7 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.7 1.0 <5 <0.2 <1 0.6 <0.2 0.1 N 12 12 12 12 12 12 12 12

114

Table A6.8 Patterson River summary statistics

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 98 36.2 16.5 1.36 0.28 Median 97 36.6 15.6 0.74 1.5 0.25 90th percentile 103 37.0 22.4 2.84 2.5 0.36 0.45 Minimum 92 >90 33.0 10.7 2.9 >3 0.49 0.17 Maximum 111 37.1 22.9 6.8 4.94 0.52 N 12 12 12 12 12 12

Total Total Total Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury SEPP objective µµµg/L <3 <5 <5 <0.15 <0.3 <7 <2.2 <0.1 Mean 2.3 Median 2.3 <0.5 <5 <0.2 <1 0.5 <0.2 <0.1 90th percentile 2.6 <0.5 <5 <0.2 <1 0.6 0.2 <0.1 Minimum 1.8 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.9 0.9 <5 <0.2 <1 0.7 0.3 0.1 N 12 12 12 12 12 12 12 12

115

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Table A6.9 Dromana summary statistics

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 97 36.5 16.1 0.63 0.23 Median 97 36.5 15.2 0.54 1.5 0.23 90th percentile 100 36.7 21.2 0.94 2.5 0.30 0.45 Minimum 93 >90 36.1 11.1 >5.0 >3 0.35 0.15 Maximum 101 36.9 22.0 >6.8 1.16 0.35 N 12 12 12 12 12 10* *insufficient number of data points to compare against SEPP objective

Total Total Total Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury SEPP objective µµµg/L <3 <5 <5 <0.15 <0.3 <7 <2.2 <0.1 Mean 2.1 Median 2.1 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 90th percentile 2.2 0.6 <5 <0.2 <1 0.5 <0.2 <0.1 Minimum 1.7 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.4 0.7 <5 <0.2 2 0.5 0.6 0.1 N 12 12 12 12 12 12 12 12

116

Table A6.10 Middle Ground Shelf summary statistics

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 97 36.6 16.4 8.3 0.75 0.18 Median 97 36.6 16.8 8.0 0.78 1.0 0.17 90th percentile 99 >90 36.9 21.0 10.3 1.09 2.0 0.22 0.35 Minimum 94 >90 36.3 11.1 5.9 >4 0.26 0.11 Maximum 100 37.0 21.4 10.5 1.19 0.25 N 12 12 12 12 12 11

Total Total Total Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury SEPP objective µµµg/L <3 <5 <5 <0.15 <0.3 <7 <2.2 <0.1 Mean 2.2 Median 2.2 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 90th percentile 2.5 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Minimum 1.7 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.6 0.7 <5 <0.2 <1 0.6 <0.2 0.1 N 12 12 12 12 12 12 12 12

117

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 6

Table A6.11 Sorrento Bank summary statistics

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 97 36.3 16.0 0.68 0.32 Median 97 36.3 16.2 0.62 1.0 0.30 90th percentile 101 >90 36.4 19.4 1.07 2.0 0.38 0.35 Minimum 95 >90 35.7 11.6 >2.9 >4 0.34 0.25 Maximum 101 36.6 21.0 >3.7 1.17 0.45 N 12 12 12 12 12 11

Total Total Total Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury SEPP objective µµµg/L <3 <5 <5 <0.15 <0.3 <7 <2.2 <0.1 Mean 2.0 Median 2.0 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 90th percentile 2.3 0.8 <5 <0.2 <1 <0.5 <0.2 <0.1 Minimum 1.7 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.3 1.0 <5 <0.2 <1 <0.5 0.4 0.1 N 12 12 12 12 12 12 12 12

118

Table A6.12 Popes Eye summary statistics

Dissolved Dissolved Secchi Secchi Chlorophyll- Chlorophyll- Oxygen Oxygen Salinity Temperature Depth Depth a a PAR PAR

SEPP SEPP SEPP SEPP objective objective objective objective attenuation attenuation %sat %sat mg/L deg C metres metres µµµg/L µµµg/L m-1 m-1 Mean 97 36.0 16.4 0.60 0.13 Median 96 35.8 16.8 0.52 1.0 0.14 90th percentile 99 >90 36.4 19.6 0.83 2.0 0.18 0.35 Minimum 93 >90 35.6 12.7 7.2 >4 0.24 0.04 Maximum 102 37.0 20.3 >12.2 0.93 0.24 N 12 12 12 9 12 11

Total Total Total Dissolved Dissolved Dissolved Dissolved Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury SEPP objective µµµg/L <3 <5 <5 <0.15 <0.3 <7 <2.2 <0.1 Mean 1.8 Median 1.8 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 90th percentile 1.9 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Minimum 1.5 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.5 0.5 <5 <0.2 <1 0.6 0.2 0.1 N 12 12 12 12 12 12 12 12

119