Baywide Water Quality Monitoring Program Milestone Report No.5

BAYWIDE WATER QUALITY MONITORING PROGRAM

MILESTONE REPORT NO.5

MARCH 2010

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 levels of accepted guidelines. EPA identified no major areas of concern from assessment of the five month reporting period, August – December 2009. 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 during this period has been noticeably influenced by the increased catchment inflows as a result of rainfall exceeding the long term monthly average in September and November 2009. 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 Executive Summary ...... 2 1. Introduction...... 7 1.1 Water Quality Baywide Monitoring Program ...... 7 1.2 Methods and Results ...... 7 1.3 Purpose of this Report ...... 8 2. Port Phillip Bay Dynamics...... 9 3. Discussion ...... 10 4. Conclusions ...... 19 5. References ...... 21 5. References ...... 21 Appendix 1 - Background...... 25 EPA’s Role in Monitoring Water Quality in Port Phillip Bay ...... 25 Appendix 2 - Methods ...... 28 Sampling Locations ...... 28 Field Sampling...... 29 Laboratory Analysis...... 31 Data Assessment Methods...... 31 External Data Sources...... 34 Appendix 3 - Results ...... 38 Field Sampling...... 38 Quality Assurance/Control (QA/QC)...... 39 Exception reports ...... 39 Results from Progress Reports ...... 39 Appendix 4 - QA/QC data and discussion...... 79 Appendix 5 - Results outside of natural/expected variability ...... 82 Appendix 6. - Summary Statistics (January – December 2009)...... 87 Appendix 7. - Errata ...... 99

List of Tables Table A1.1 SEPP (WoV) objectives and ANZECC trigger values ...... 27

Table A2.1 Locations and corresponding SEPP (WoV) segments...... 28 Table A2.2 EWMA control limits for listed water quality parameters ...... 32 Table A2.3 Shewhart control limits for listed water quality parameters ...... 33

Table A3.1 Field sampling dates and weather conditions (August – December 2009) ...... 38 Table A3.2 Summary of Exception Reports (August – December 2009) ...... 39 Table A3.3 Summary of exceedence of control limits for physico-chemical data and nutrients (August – December 2009) ...... 41 Table A3.4 Summary of exceedence of control limits for metals (August – December 2009)...... 42 Table A3.5 Temperature stratification in PPB (August – December 2009) ...... 53 Table A3.6 Phytoplankton, chlorophyll-a and chlorophyll fluorescence at the Yarra River at Newport (November – December 2009) ...... 71

Table A4.1Nutrient replicate results outside of the laboratory MU (August – December 2009)...... 81

Table A5.1 PoMC Assessment (August - December 2009) ...... 83

Table A6.1 Yarra River at Newport summary statistics – Schedule F7 Yarra Port Segment Objectives...... 87 Table A6.2 Yarra River at Newport summary statistics – Schedule F6 Hobsons Segment objectives...... 87 Table A6.3 Hobsons Bay summary statistics ...... 89 Table A6.4 Corio Bay summary statistics...... 90

Table A6.5 Long Reef summary statistics...... 91 Table A6.6 Central Bay summary statistics...... 92 Table A6.7 POM DMG summary statistics...... 93 Table A6.8 Patterson River summary statistics...... 94 Table A6.9 Dromana summary statistics...... 95 Table A6.10 Middle Ground Shelf summary statistics...... 96 Table A6.11 Sorrento Bank summary statistics...... 97 Table A6.12 Popes Eye summary statistics ...... 98

Table A7.1 Summary of changes to metals values reported in Progress Report No.1...... 99 Table A7.2 Summary of changes to arsenic EWMA values reported in Milestone Reports No.1 and 2 and Progress Report No.3...... 100

List of Figures Figure 1 Water Quality Monitoring Program sampling sites in PPB ...... 8

Figure A2.1 DPI Nutrient cycling continuous in-situ monitoring sites ...... 35 Figure A2.2 Examples of IMOS shipborne data sampled from the Spirit of Tasmania...... 36 Figure A2.3 EPA and PoMC Beach monitoring sites ...... 37

Figure A3.1 2009 Victorian rainfall deciles January – June 2009 and July – December 2009 ...... 43 Figure A3.2 Yarra River rainfall, river flow and storm events August – December 2009...... 44 Figure A3.3 Patterson River rainfall and storm events August – December 2009...... 44 Figure A3.4 Victorian rainfall totals for August - December 2009...... 45 Figure A3.5 IMOS shipborne data from Port Melbourne (November – December 2009)...... 46 Figure A3.6 IMOS shipborne track data (November 21 - 26 2009) ...... 46 Figure A3.7 Surface water temperature at Hobsons Bay (August – December 2009) ...... 47 Figure A3.8 Central Bay surface and bottom water temperature (August – December 2009)...... 47 Figure A3.9 IMOS shipborne water temperature measurements for PPB (September – December 2008 and 2009)...... 48 Figure A3.10 Annual rainfall and average salinity measurements for PPB (1986 – 2009)...... 48 Figure A3.11 Average salinity for PPB (November 2007 – December 2009)...... 49 Figure A3.12 Central Bay surface salinity and dissolved oxygen measurements (August - December 2009) ...... 49 Figure A3.13 Salinity CTD profiles for the Yarra River at Newport (August – December 2008 and 2009) ...... 50 Figure A3.14 IMOS shipborne salinity measurements for PPB (September – December 2008 and 2009)...... 51 Figure A3.15 Yarra River at Newport temperature and salinity stratification (October 2009) ...... 52 Figure A3.16 Temperature profiles from Hobsons Bay, Central Bay and PoM DMG (November 2009) ...... 52 Figure A3.17 Hobsons Bay dissolved oxygen measurements (August – December 2009) ...... 54 Figure A3.18 Water clarity (Secchi depth) at Yarra River at Newport (November 2007 – December 2009 ...... 55 Figure A3.19 Historical and current Secchi depth data for the Yarra River (December 2004 – December 2009)...... 55 Figure A3.20 Yarra River at Newport CTD turbidity profile August – December 2009 ...... 56 Figure A3.21 IMOS shipborne turbidity measurements for PPB (September to December 2008 and 2009) ...... 57 Figure A3.22 Secchi depth and TSS at Yarra River at Newport (November 2007 – December 2009)...... 57 Figure A3.23 Ammonium EWMA control chart for Dromana (November 2007 – December 2009)...... 58 Figure A3.24 Ammonium Shewhart control chart for Dromana (November 2007 – December 2009)...... 59 Figure A3.25 NOx EWMA control chart for MGS (November 2007 – December 2009) ...... 59 Figure A3.26 NOx EWMA control chart for Corio Bay (November 2007 – December 2009)...... 60 Figure A3.27 NOx Shewhart control chart for Corio Bay (November 2007 – December 2009)...... 60 Figure A3.28 NOx Shewhart control chart for Central Bay (November 2007 – December 2009)...... 61 Figure A3.29 NOx EWMA control chart for Central Bay (November 2007 – December 2009)...... 61 Figure A3.30 NOx Shewhart control chart for Yarra River at Newport (November 2007 – December 2009) ...... 62 Figure A3.31 NOx EWMA control chart for Yarra River at Newport (November 2007 – December 2009)...... 62 Figure A3.32 Total nitrogen Shewhart control chart for Yarra River at Newport (November 2007 – December 2009) .....63 Figure A3.33 Total nitrogen EWMA control chart for Yarra River at Newport (November 2007 – December 2009) ...... 63

Figure A3.34 Phosphate Shewhart control chart for Hobsons Bay (November 2007 – December 2009) ...... 64 Figure A3.35 Phosphate EWMA control chart for Hobsons Bay (November 2007 – December 2009) ...... 64 Figure A3.36 Total Phosphorous Shewhart control chart for PoM DMG (November 2007 – December 2009)...... 65 Figure A3.37 Total Phosphorous EWMA control chart for PoM DMG (November 2007 – December 2009)...... 65 Figure A3.38 Silicate control chart for Yarra River at Newport (November 2007 – December 2009)...... 66 Figure A3.39 Silicate control chart for Patterson River (November 2007 – December 2009)...... 66 Figure A3.40 Total phytoplankton cell numbers across PPB (February 2008 – December 2009)...... 67 Figure A3.41 Phytoplankton and nutrient levels at the Yarra River at Newport (January - December 2009) ...... 68 Figure A3.42 Hobsons Bay surface Chlorophyll-a measurements (August – December 2009) ...... 68 Figure A3.43 IMOS shipborne in-situ chlorophyll fluorescence measurements for PPB (September – December 2008 and 2009)...... 69 Figure A3.44 Interpolated chlorophyll-a data (January – December 2009) ...... 70 Figure A3.45 Total phytoplankton cell count and chlorophyll-a concentrations at the Yarra River at Newport site (November 2007 – December 2009)...... 71 Figure A3.46 Number of taxa recorded at Long Reef and Popes Eye (January to December 2009)...... 72 Figure A3.47 Arsenic Shewhart control chart for Central Bay (November 2007 – December 2009)...... 73 Figure A3.48 Arsenic EWMA control chart for Central Bay (November 2007 – December 2009)...... 73 Figure A3.49 Arsenic Shewhart control chart for Corio Bay (November 2007 – December 2009)...... 74 Figure A3.50 Comparison of arsenic data from the Melbourne Water, EPA Beach and Water Quality monitoring programs (January – December 2009)...... 75 Figure A3.51 Total chromium Shewhart control chart for Yarra River at Newport (November 2007 – December 2009)... 76 Figure A3.52 Dissolved zinc control chart for Yarra River at Newport (November 2007 – December 2009)...... 77 Figure A3.53 Total zinc Shewhart control chart for Yarra River at Newport (November 2007 – December 2009)...... 77 Figure A3.54 Comparison of zinc data from the Melbourne Water, EPA Beach and Water Quality monitoring programs (January – December 2009)...... 78

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 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 PAR Photosynthetic Active Radiation PoM DMG Port of Melbourne Dredge Material Ground PoMC Port of Melbourne Corporation PPB Port Phillip Bay 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 4.0 (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 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 QA/QC 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).

Figure 1 Water Quality Monitoring Program sampling sites in PPB

1.3 Purpose of this Report

Milestone Report # 5 (this report) is required under the Water Quality Detailed Design (PoMC 2010a) and describes the water quality monitoring component of the BMP for the five month reporting period from August – December 2009 inclusive, while also reflecting on the program to date (November 2007 – December 2009). 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) 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).

2. PORT PHILLIP BAY DYNAMICS

Port Phillip Bay (PPB) is shallow (<25 m deep) and large (2,000 km 2) in relation to its catchment (about 10,000 km 2). 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 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 predominately 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 discharge flows 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 N 2 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).

3. 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 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 in supporting nitrification and suppressing denitrification. Water clarity and TSS are related, and are measured because of their impact on light availability for plants, as well as aesthetics.

Salinity, temperature, dissolved oxygen

Salinity, temperature and DO throughout PPB during the reporting period (August-December 2009) were within expected natural variability and SEPP (WoV) objectives. Increased rainfall and associated catchment inflows influenced salinity across the whole of the Bay, with the lowest average salinities seen since the commencement of the WQBMP (Figure A3.11). As expected, the Yarra River at Newport site was most strongly influenced by the increased catchment flows. Temperature profiles across the Bay show water temperatures in late 2009 are warmer than the same period in 2008 (Figure A3.9), with a sharp increase evident in water temperatures associated with the unseasonably warm weather in November. DO concentrations in surface waters met SEPP (WoV) objectives, while periods of low DO in bottom waters were short-lived.

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 affects 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. Salinity in PPB is influenced by freshwater inflows, patterns of circulation and water exchange with Bass Strait. Since the onset of drought conditions in Victoria (extending for more than a decade), freshwater inflows to the Bay have been reduced. Average salinity levels have consequently risen to greater than that of Bass Strait (Figure A3.10). Rainfall in the catchments surrounding PPB was above the long term average for September and November 2009. In particular, rainfall in November 2009, which exceeded 100mm, was almost double the long-term average (Figure A3.4; Bureau of Meteorology 2009a). This increase in rainfall was reflected in flows in the Yarra River (and ultimately discharges of freshwater to the Bay), which peaked in September and November 2009 (Figure A3.2). The increase in freshwater inflows affected concentrations of salinity across the Bay, with average salinity levels decreasing during the reporting period (Figure A3.11). The effect was most pronounced at sites close to freshwater discharge points (Yarra River at Newport and Patterson River). The Integrated Marine

Observation System (IMOS) shipborne data show the extent of the Yarra River flows, with the salinity contour penetrating further south into PPB than for flows during 2008 which were confined to Hobsons Bay (Figure A3.14). The Bay is still hypersaline, with salinity above the long-term (1984-2007) average, and also above the more recent (2002-07) drought average.

The increase in freshwater inflows during the reporting period also resulted in stratification of the water column at the Yarra River site. A halocline was evident at the Yarra River at Newport site in every month from August to December 2009 (Figure A3.13), but the only occasion where this coincided with reduced DO concentrations in the bottom waters was December 2009, when DO was < 80% saturation at depth. This reduction in DO coincided with an increase in phytoplankton biomass and later decomposition. By definition of the Detailed Design (PoMC 2010a), salinity stratification (> 10 psu difference between surface and bottom waters) occurred only during October 2009 (Figure A3.15). Reduction in DO can adversely affect aquatic fauna, and the SEPP (WoV) guideline for DO is >90% to protect fauna from such affects. DO concentrations fluctuate considerably over diurnal cycles, and instantaneous measures of DO are not considered to be a very useful measure of ecosystem health and function (ANZECC 2000). Results from the DPI Nutrient Cycling Baywide Monitoring Program show the variability that can occur in DO concentration that is not evident in single samples collected for the WQBMP (Figure A3.17). Continuous measurements near the seabed, as collected by DPI, are also more likely to detect the effects of thermal or salinity stratification on DO, compared with monthly measurements from surface waters. Elevated DO was observed in Hobsons Bay surface waters following the flood events, with low DO concentrations in bottom waters. These variations with depth relate to flood-enhanced plankton growth and subsequent decay (Longmore and Nicholson 2010). Temperature throughout the reporting period followed expected patterns, with an increase of 10-12 °C from winter to summer months. Temperature stratification (> 0.5°C difference between surface and bottom waters; PoMC 2010a) occurred at a number of sites (Table A3.5). Visual assessment of the profile data indicates that of the 19 instances listed in Table A3.5, only six show a marked thermocline rather than a gradual decline in temperature with depth. The strongest of these was during November 2009 when there was ~3.5 °C temperature difference between surface and bottom water at Hobsons Bay, Central Bay and Port of Melbourne Dredge Material Ground (PoM DMG), with a distinct thermocline at a depth of about 5-10 metres (Figure A3.16). These instances of temperature stratification at Hobsons Bay, Central Bay and PoM DMG also coincided with changes in DO at depth, with a 5-10% reduction in DO between surface and bottom waters. In general, temperature stratification in PPB is most common from August to February, when the air temperature exceeds water temperature (Black and Mourtikas 1992). Water temperature increased sharply between the October and November 2009 water quality sampling events, with the DPI monitoring data indicating the sharpest increase of 4–5 °C occurred from 7 to 10 November (Figure A3.7). During November 2009, Melbourne experienced unseasonably hot weather conditions, with a large number of days >30 °C. Sampling occurred between November 10 and 12, during a period of seven consecutive days of maximum temperatures above 30 °C, minimum temperatures close to 20 °C and increased hours of sunlight (Figure A3.7). Combined with relatively calm conditions, this scenario undoubtedly contributed to the stratified conditions during the reporting period. Differences in surface and bottom waters only persisted for 5-10 days before being broken down by mixing events (Figure A3.8).

Water clarity and total suspended solids

Water clarity (as measured by Secchi depth and turbidity) was generally good across the Bay, with SEPP (WoV) objectives met at most sites during the reporting period (August-December 2009). The notable exception was the Yarra River at Newport site, where the SEPP (WoV) objective has not been met for most of the WQBMP to date. Water clarity at this site has historically not met SEPP (WoV) objectives, particularly during periods of high flow and storm events. A decrease in turbidity levels occurred in late 2009 when compared to late 2008, despite increased catchment flows (Figure A3.21). This relative decrease in turbidity levels is likely to be a result of reduced dredging activities in the Bay.

In the context of PPB, water clarity is important in terms of sufficient light availability for primary production, and also for aesthetic purposes. In addition, the amount of suspended particulate matter in the water column (as indicated by TSS concentrations) can influence the health of aquatic fauna by the physical action on gills (Jenkins and McKinnon 2006).

Turbidity, Secchi depth, TSS and light are all measures that are related to water clarity. The relationship between each measure is not necessarily direct or linear (Davies-Colley and Smith 2001). An increase in suspended solids will result in a decrease in light and Secchi depth, while properties of 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). It is therefore pertinent to consider at least one direct measure of water clarity, and also suspended sediments, due to their different biological effects. During the reporting period (August - December 2009), water clarity (as indicated by Secchi depth) at most sites was within historical values and SEPP (WoV) water quality objectives. The exceptions were the Yarra River at Newport (multiple occasions) and Patterson River (one occasion) sites. The latter of these was a marginal exceedence (by 0.1 m) that did not persist (Table A3.3). The Secchi depth at the Yarra River at Newport site did not meet the SEPP (WoV) objective of >2m on every sampling event since July 2008, and has only been within the limit on six occasions out of the 26 sampling events since November 2007 (Figure A3.18). This is likely to have been influenced, at least in part, by dredging activities for the CDP, and is consistent with the predicted effects of the SEES. The limited historical data for Secchi depth from the Yarra River at Newport site indicate that there are periods of low water clarity experienced at this site in the absence of dredging (Figure A3.19). The Yarra River historically is considered to be turbid, with approximately 41,000 tonnes of sediment transported annually (DSE 2006). During high flows and storm events, large amounts of sediment are transported from urban and rural catchments in the Yarra River and discharged into PPB (Sokolov 1996). It is likely that high flows in the Yarra that occurred in September and November 2009 would have influenced water clarity at the Yarra River at Newport site during the reporting period. Despite the duration of low (below SEPP (WoV)) water clarity at the Yarra River at Newport site, the effects were localised and did not extend further into PPB. The SEPP (WoV) objectives for Secchi depth in Hobsons Bay were met for the entire reporting period (August to December 2009). The Yarra River at Newport is the only site in which there is a SEPP (WoV) objective for TSS. This is a result of the anomaly within the northern boundary of SEPP (WoV) Schedule F6, where the latitude/longitude puts this site in the Hobsons segment, while ‘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 River at Newport site. TSS concentrations have closely followed the pattern of Secchi depth at the

Yarra River at Newport site since the commencement of the WQBMP in November 2007 (Figure A3.22). Unlike Secchi depth, TSS concentrations have remained well within the SEPP (WoV) objective of < 25 mg/L (annual median) and < 60 mg / L (annual 90 th percentile). Average TSS concentrations showed a spatial gradient declining through Hobsons Bay into PPB during the reporting period. These observations are consistent with the Bay having typically low turbidity and suspended solids, particularly in the centre and south of the Bay, grading to higher turbidity and suspended solids in the north of the Bay. The IMOS shipborne turbidity data show higher turbidity levels (3-4NTU) associated with trailing suction hopper dredger (TSHD) dredging activities in September, October and December 2008, compared to periods when dredging was either minor (grab/backhoe dredge) or absent such as in November 2008 and late 2009 (Figure A3.21). Short-term periods of elevated turbidity measuring 10-40 NTU were evident during the late 2008 period within Hobsons Bay, with the most extensive plume associated with enhanced Yarra River flow in late November 2008. In contrast, the short-term peaks in turbidity in Hobsons Bay during late 2009 were lower, measuring 5-10 NTU, which also coincided with Yarra River flows.

Nutrients

Because plant growth in PPB is nitrogen-limited (Harris et al . 1996), there is a hierarchy of interest in considering the various nutrient forms. Of particular interest, in terms of plant growth, are the dissolved inorganic nitrogen forms, ammonium, nitrite and nitrate, because they are the most readily taken up by plants. Silicate (Si) 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 (N) and phosphorus (P) are also of lesser interest, as they are generally not readily available for uptake by plants. Nutrients in aquatic ecosystems are significant for the role they play in primary production. Deciphering patterns and trends of 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. nitrate plus nitrite (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). 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 water exchange rates with Bass Strait (Harris et al . 1996). Dredging can also result in the release of nutrients stored in the sediment as well as affecting the denitrification cycle (Longmore 2006). 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. Rather, the effects of increased nutrients are assessed through their primary response (increased phytoplankton production) with SEPP (WoV) objectives for chlorophyll-a concentrations. Assessment of nutrients for the WQBMP is via EWMA and Shewhart control limits.

While the measured nutrients in the period August to December 2009 were within control limits at most sites on most occasions, there were exceedences of limits at some sites. Isolated, one-off breaches of control limits are difficult to interpret, for the reasons described above.

Nitrogenous compounds

The spatial variation observed in nitrogen concentrations (total nitrogen, ammonium and NOx) during the reporting period (August - December 2009) is consistent with previous observations (Harris et al. 1996), with highest concentrations close to the known major nutrient sources (WTP and the Yarra River). Winter peaks in NOx, attributed to Bass Strait waters, were again observed in the south of the Bay.

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 plankton 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. Ammonium concentrations at all sites, with the exception of Dromana, were similar to the historical mean and below Shewhart and EWMA control limits during the current reporting period. December 2009 was the first month since the commencement of the WQBMP that the EWMA values at Dromana dropped below the control limit of 5 µg/L (Figure A3.23). Ammonium levels at Dromana have continued to show a decreasing trend since March 2009 (Figure A3.24), with concentrations moving closer to the historical mean value. Isolated exceedences of NOx control limits were reported at Corio Bay, Central Bay and Middle Ground Shelf (MGS) during the reporting period. The short term increases in NOx at Corio Bay (Figure A3.27) and Central Bay (Figure A3.28) continued to influence the EWMA for several months (Figure A3.26 and Figure A3.29 respectively). The increase in NOx was limited in both space and time, and is unlikely to have resulted in ecological effects of any consequence to PPB as a whole. A peak in NOx at MGS also influenced the EWMA values at this site (Figure A3.25) during the reporting period. The concentrations of NOx remained low (relative to the north of the Bay), but peaks have been observed in winter in the south of PPB previously (EPA 2009o). These peaks have been attributed to inflows of Bass Strait water, which may have increased in recent years as a result of drought-induced changes to water exchange with Bass Strait (EPA 2009o). The recurrence of increased NOx at southern sites during winter is similar to the pattern observed in chlorophyll-a at southern sites, with increased biomass in winter months. There is no direct correlation between the measured concentrations of NOx and chlorophyll-a at this or any other southern site, although the pattern of higher concentrations suggests the increased NOx inflows have an effect on primary production in the south of the Bay. NOx concentrations at Yarra River at Newport exceeded the EWMA control limit from August to December 2009 (Figure A3.31), and total nitrogen at this site was above the EWMA control limit from September to December 2009 (Figure A3.33). In addition, a peak in NOx exceeded the Shewhart limit in October 2009 (Figure A3.30), and total nitrogen peaks exceeded this short term limit in both October and December 2009 (Figure A3.32). These peaks in NOx and total nitrogen in October coincided with storm events and increased flows down the Yarra River (Figure A3.2), indicating upstream catchments as the most likely source of both particulate and dissolved nitrogen.

Phosphorous compounds and silicate

Phosphorous concentrations throughout the Bay continued to decline during the reporting period (August - December 2009). Spatial variability in phosphorous concentrations followed historical patterns, with highest concentrations found adjacent to the WTP and lowest levels in the south of the Bay. Silicate concentrations were highest at sites close to the Yarra and Patterson Rivers following periods of high river flow.

The WTP is the principal source of phosphorus to the Bay (900-1,500 t y -1 between 1996 and 2006; 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 thus shows concentrations decreasing in the following order of sites: Long Reef, Corio Bay, Yarra River at Newport and Hobsons Bay, Central Bay and near shore PPB, and south of the Sands. Both phosphate and total phosphorus concentrations are continuing the downward trend identified during the previous reporting period (February to July 2009) (Figure A3.35 and Figure A3.37). All results were below the Shewhart control limits and generally below the historical mean (Figure A3.34 and Figure A3.36). The decline is not a recent phenomenon. The mean phosphate concentration at the Central Bay site declined from 70 µg/L in 1984-99 to 60 µg/L in 2001-06, dropping to 43 µg/L in 2008-09. The distribution of phosphorus in PPB is governed by dilution, and most phosphorus is lost through flushing to Bass Strait. The flushing rate of PPB associated with catchment inflows has declined during drought conditions, while inflows of Bass Strait water have increased in recent years as a result of these drought- induced changes. Bass Strait waters have a much lower concentration of phosphorus than Bay waters, and increased inflows from Bass Strait may have reduced phosphate concentrations in the south of the Bay. The observation of declining concentrations throughout the remainder of the Bay (remote from the Bass Strait influence) indicates that the catchment input has declined. The observed decline in phosphate concentration is not a factor in limiting the productivity of PPB. Phytoplankton (specifically diatoms) require nutrients in atomic ratios N:P:Si 16:1:18 (Harris et al . 1996). Analysis of the water quality monitoring program nutrient data indicates that the N:P ratio has been well below 16 at all sites in all months. Plankton growth has been and still remains strongly nitrogen-limited, despite the decline in phosphate concentration. The N:Si ratio at all sites except Long Reef also indicates nitrogen is more limiting than silicate. The N:Si ratio at Long Reef falls below 1:1 in winter of each year, indicating silicate limitation of diatom growth is possible. This is at the time of peak nitrogen discharge from the WTP, and as the nitrogen discharge declines in spring, nitrogen limitation is again established. There are no control limits or SEPP (WoV) objectives for silicate. Highest silicate concentrations were reported at the Yarra River at Newport site (Figure A3.38), with a peak in silicate also reported at Patterson River in December 2009 (Figure A3.39). The major source of silicate to PPB is freshwater runoff, principally the Yarra River (Murray and Parslow 1997), and most of the high silicate concentrations followed periods of high river flow.

Phytoplankton and chlorophyll-a

Phytoplankton and chlorophyll-a concentrations were consistent with historical patterns during the reporting period (August –December 2009), with the greatest biomass occurring in the north of the Bay. The spring/summer catchment flows in the Yarra River carrying nutrients stimulated phytoplankton growth in this section of the Bay, while biomass remained low in the south of the Bay. The pattern of species richness is the inverse of phytoplankton abundance, with greatest species richness recorded in the south of the Bay.

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 reporting period, was consistent with these historical trends of spatial and temporal variability (Figure A3.44). SEPP (WoV) water quality objectives of chlorophyll-a are based on annual medians and 90 th percentiles to integrate seasonal variability. Annual medians and 90 th percentiles for chlorophyll-a calculated over the period January to December 2009 were within SEPP (WoV) objectives at all sites with the exception of the Yarra River at Newport (Table A6.2). The exceedence of the SEPP (WoV) objective at this site is a reflection of the increased phytoplankton biomass recorded at this site in December 2009. During the reporting period, the EWMA control limit was exceeded at two sites, Yarra River at Newport in December and MGS in August 2009, reflecting the seasonal trends in phytoplankton biomass described above. Dominant species contributing to biomass at these sites at the time of the exceedences were also consistent with historical trends (as described by Arnott et al .1997), with diatoms dominating the summer “bloom” in the Yarra River and flagellate cryptophytes the dominant taxonomic group at MGS in August. Modelling (Parslow et al. 1999) and previous observations (Harris et al . 1996) suggest that spring/summer high flow events in the Yarra, which deliver a large proportion of the annual nutrient load, should stimulate phytoplankton growth. Phytoplankton populations (dominated by Skeletonema japonicum/pseudocostatum ) increased in the Yarra River and Hobsons Bay in November 2009 and in the Patterson River in December (Figure A3.40). This increase followed a large storm event (and increased river flows) in October and late November 2009 (Figure A3.2 and Figure A3.3). This influx of freshwater carried increased nutrient loads into PPB with peaks in nitrogenous compounds and silicate observed in October 2009 at the Yarra River at Newport site. Nutrient concentrations then dropped considerably in November following uptake by phytoplankton (Figure A3.41). The pattern may be indicative of the “bloom” originating in the Yarra River and moving to Hobsons Bay and then down the east coast of the Bay, or it could be the result of discrete populations of phytoplankton responding to increased nutrients from freshwater discharges. As there is no

information on phytoplankton community composition or abundance along the east coast of the Bay between Hobsons Bay and the Patterson River, it is not possible to confirm this hypothesis. The Nutrient Cycling Baywide Monitoring Program also identified a smaller increase in phytoplankton biomass ( in-situ chlorophyll fluorescence) in Hobsons Bay and Long Reef in September 2009 associated with increased river (Yarra and Werribee) flows. This increase was not recorded by the WQBMP (Figure A3.42). Peaks in chlorophyll-a concentration lagged peak river flows by 5-10 days, indicating the short time needed to convert nutrients from the catchment into plant biomass. Longmore and Nicholson (2010) noted that the phytoplankton response to the high flow in November was less than that to the earlier (September) high flow, in part because the earlier event is likely to have flushed more of the catchment than the later event, and also because the nutrient pools in the catchment may not have been fully restored in the two months between events. Neither of the high flow events appeared to have affected denitrification efficiency in Hobsons Bay (Longmore and Nicholson 2010). The November 2009 benthic flux measurements were taken only two days after the heaviest rainfall in a year (48 mm on 22 November) for the area, and algal growth had not yet increased by the December monitoring event. The extent of impact (and speed of recovery) from the November high-flow event may be better understood once data from the January monitoring event and recent Nutrient Cycling Monitoring Program logger deployment are reported. Phytoplankton enumeration data from the Yarra River at Newport did not always correspond with the chlorophyll -a data during the reporting period. The peak in chlorophyll-a in December corresponded with average cell numbers, and lagged behind a peak in cell numbers in November (Figure A3.45). This disparity between cell counts and chlorophyll-a concentrations is common in the data collected for the WQBMP (EPA 2009n). There are a number of possible explanations for the inconsistency in chlorophyll-a concentrations and cell counts. It may be due to the different sampling procedures (surface samples for chlorophyll-a compared to integrated samples across the water column for phytoplankton) or the different species of phytoplankton that can contain different amounts of chlorophyll-a depending on their size, dominant pigments and responses to environmental variables such as light and temperature. Cryptophytes were the most numerous taxonomic group within the phytoplankton community at all sites in August 2009, with the exception of Corio Bay, where diatoms comprised > 40% of total cells. By November and December 2009, there had been a shift in community composition, where diatoms dominated. In the south of the Bay, although diatom numbers increased to greater proportions than evident in winter, small flagellates (Cryptophytes, Prasinophytes and Prymnesiophytes) occurred in greater abundances. The most abundant species was Skeletonema japonica/pseudocostatum ; but this was heavily skewed by extreme numbers of these taxa in “blooms” in the Yarra River, Hobsons Bay and Patterson River. Although potentially harmful species have been recorded in relatively high abundances on occasion in PPB (Magro, et al. , 1997; Nicholson et al ., 1998), there were no incidences of potentially harmful species above control limits during this reporting period. Species richness (number of taxa) during the period varied considerably across sites and sampling events. Total number of taxa ranged from a low of 27 at Patterson River (November) to a high of 51 at Sorrento (October) and Pope’s Eye (November). Mean number of taxa recorded was highest at Popes Eye (43.6) and lowest at Long Reef (35.8). This is exactly the opposite of the previous reporting period (February to July 2009). If an entire annual cycle is considered, the differences in number of taxa recorded at each site is more even, with annual mean taxa numbers ranging from 36 to 39. The pattern of species richness is the inverse of phytoplankton abundance, with greatest species richness recorded during times of lowest abundance (Figure A3.46).

Metals

Metal concentrations generally remained low throughout the Bay during the reporting period (August - December 2009), consistent with historical results. Elevated zinc concentrations were recorded in the north due to the influence of the Yarra River flows. The reported detection of mercury above the SEPP (WoV) objective in November 2009 was transitory and within acceptable levels when considering the measurement of uncertainty.

Heavy metals in the waters of PPB, with the exception of arsenic, are low compared to ranges found in other estuaries, and close to values for other 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 sediment acts primarily as a sink for heavy metals, but shipping, storm events and dredging can result in disturbance of the sediment and re-suspension of metals into the water column (Fabris et al . 1995).

Dissolved mercury concentrations were reported at 0.1 µg/L at all sites in November 2009, which is equal to the laboratory Limit of Reporting (LOR). Because SEPP (ANZECC) requires mercury levels to be <0.1 µg/L, this resulted in a number of exceedences (Table A3.4). When considering the measurement of uncertainty (0.115 µg/L) associated with these results, the mercury concentrations were within acceptable limits. Similar results were reported for the weekly monitoring occurring at the beaches in and around Hobsons Bay (OEM 2010). Zinc concentrations in the dissolved state were above the SEPP (ANZECC) objective at the Yarra River at Newport site in August and December 2009 (Figure A3.52). Particulate (and more rarely dissolved) zinc has exceeded the objective at this site on a number of occasions throughout the WQBMP (Figure A3.53). The lower Yarra River is known to have elevated concentrations of zinc in the sediment and the water column compared to the rest of the Bay. Fabris et al . (1995) suggested that this was attributed to catchment inputs from the Yarra River. This is supported by the data collected in the Melbourne Water monitoring program that show high levels of zinc present in the river system (Figure A3.54). The sediments carrying metals can be released into the water column by storm events, wave action, shipping and dredging. It is likely that a combination of factors have resulted in the isolated incidences of elevated dissolved zinc in the Yarra port area. Concentrations are still many orders of magnitude below that known to cause direct toxicity to humans, and below critical ecological effects thresholds (ANZECC 2000). Arsenic concentrations, which had been reported above the EWMA control limits at a number of sites during previous reporting periods (EPA 2009m; n) have dropped below the EWMA control limit during this reporting period at all sites (Figure A3.47 and Figure A3.48). PPB arsenic concentrations are at the high end of those reported elsewhere in the world. The origin of the high arsenic in PPB is not well understood, but Fabris and Monahan (1995) proposed that some process in the sediments was releasing arsenic to the water column. Various data support this proposal. First, seasonal variations in arsenic are evident from the monthly sampling, particularly in Corio Bay (Figure A3.49), and as demonstrated by Emphron (2009) from results of the weekly sampling of 36 beaches in PPB between March 2008 and September 2009. Second, while the Melbourne Water monitoring data shows that arsenic concentrations within the Yarra and Maribyrnong Rivers are of the same relative order as PPB, there is no evidence of seasonal variations consistent with that recorded in PPB waters (Figure A3.50).

4. 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 levels of accepted guidelines.

A summary of results from the current reporting period August – December 2009 are presented below:

• Increased catchment inflows associated with the above average rainfall conditions during September and November (Figure A3.1) have noticeably influenced water quality in PPB. • The increase in freshwater inputs affected concentrations of salinity across the Bay with average salinity levels decreasing in the latter half of 2009. These levels are still above the long-term average. • There was an evident halocline at the Yarra River at Newport site in every month from August to December 2009 associated with increased Yarra River flows. • Temperature throughout the reporting period generally followed expected patterns with an increase of 10 - 12 °C from winter to summer months. • Unseasonably hot weather conditions in November caused a rapid rise in water temperatures resulting in short term temperature stratification occurring at a number of sites. • At all sites except Yarra River at Newport, water clarity (as measured by Secchi depth) was within historical measures and SEPP (WoV) objectives. • Water clarity at Yarra River at Newport was influenced by increased catchment inflows and dredging activities. • Despite increased catchment inflows, turbidity levels in PPB are low. The low levels are consistent with the cessation of dredging in late 2009. • The spatial variation in nitrogenous compounds is generally consistent with previous observations with highest concentrations close to the known major nutrient sources (WTP and the Yarra River). • The observed decline in concentrations of phosphorous compounds is not a factor in limiting the productivity of PPB. • Phytoplankton populations (dominated by Skeletonema japonicum/pseudocostatum ) increased in the north of PPB in November and December in response to increased catchment inflows and associated nutrient loads. • The pattern of phytoplankton species richness is the inverse of phytoplankton abundance, with greatest species richness recorded during times of lowest abundance. • Concentrations of heavy metals in the waters of PPB were generally low and consistent with previous 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.

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.

5. REFERENCES

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EPA 2009n. Baywide Water Quality Monitoring Program Report No 4. October 2009, EPA. EPA 2009o. Internal EPA Filenote: Review of nitrogen levels in the south of Port Phillip Bay , December 2009

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

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. 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, 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 and Nicholson 2010 . 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. 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. Murray, A. and Parslow, J., 1997, Port Phillip Bay Integrated Model: final report. Technical Report No. 44, CSIRO Port Phillip Bay Environmental Study, ACT. Nicholson, G, Arnott, G, Longmore, A, Sporcic, M 1998. Dynamics of harmful Rhizosolenia cf. chunii blooms in Port Phillip Bay . Final Report on project 96/264 to Fisheries Research and Development Corporation. Marine and Freshwater Research Institute: Queenscliff.

OEM 2010. Port of Melbourne Maintenance Dredging, http://www.oem.vic.gov.au/Maintenancedredging accessed February 10, 2010 Parslow J, Murray A, Andrewartha J, Sakov P 1999. Port Phillip Bay integrated model scenarios of nitrogen load reductions and aquaculture loads. Final Report to Victorian NRE . CSIRO, Hobart. 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 4.0 , Port of Melbourne Corporation.

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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. Wood, M. and Beardall, J., 1992, Phytoplankton Ecology of Port Phillip Bay, Victoria, Port Phillip Bay Environmental Study, Technical Report No.8, CSIRO, Melbourne.

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.

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 Min for Min for surface 1m below Min 1m above bottom limitLower for percentile 90th 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 ( Cadmium Nickel ( Chromium Chromium ( Zinc ( Copper ( Copper TBT ( Lead ( Lead Mercury (

>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.

*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 0.45 µm 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 10 units) 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. • One seawater field blank per cruise to test for laboratory precision. • 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 2009/2010 EPA Quality Plan 5 is the key document that outlines all relevant QA/QC specifications for the EPA WQBMP. This includes the QA/QC 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 2009, EPA Victoria Baywide Water Quality Monitoring Program Quality Plan

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 QA/QC programs while the EPA also conducts cross laboratory analyses 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 2009, 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.

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 5

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 4.0 (available on the CDP website www.channelproject.com ).

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 4.0, (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, PoMC leads an assessment of the significance to the environment, with the support of EPA. If results are significant, this initiates further risk-based assessments in accordance with the Water Quality Detailed Design CDP_ENV_MD_023_Rev 4.0, 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

External Data Sources

This report also includes data from concurrent water quality monitoring undertaken continuously in PPB during the reporting period. 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. 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: • Hobsons Bay

8 PoMC 2010. Water Quality – Detailed Design CDP_ENV_MD_023 Rev 4.0 , Port of Melbourne Corporation. 9 PoMC 2009. Algal Blooms – Detailed Design CDP_ENV_MD_012 Rev 3.0 , Port of Melbourne Corporation.

• 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 for the August – December 2009 reporting period 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 4.0, 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

10 PoMC 2010. Nutrient Cycling Detailed Design CDP_ENV_MD_019 Rev 4.0 , Port of Melbourne Corporation.

2008 and provided an unbroken record through to July 2009, when the vessel was taken offline. The system was back online 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 ~20 knots this corresponds to sample “grabs” at every 100m along the ship track. Such high repeat sampling 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 The data sampled off the Spirit of Tasmania 1, is referred to in this report as IMOS shipborne data. Contoured sensor data for the September to December 2009 and comparative September to December

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 .

2008 reporting period is presented in the following results section as shiptrack distance in PPB (from Port Melbourne Pier) against date. Each plot represents data from ~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 year-round 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. 13 As part of the PoMC routine maintenance dredging program, water from six northern PPB beaches is monitored for heavy metals (Figure A2.3). The monitoring program commenced on 17 th November 2009 with weekly testing to continue until 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 .

APPENDIX 3 - RESULTS

This Milestone Report (#5) incorporates all data collected since the inception of the program in November 2007 with the focus primarily on this reporting period extending from August - December 2009.

Field Sampling

Field sampling was conducted monthly as outlined in Table A3.1. Capital dredging using a trailing suction hopper dredger (TSHD) was occurring in the South Channel and Yarra River up to the 2 nd September 2009. From this time until the completion of the dredging activities on 2 nd November 2009 only minor dredging was undertaken using a backhoe/grab dredge. The maintenance dredging program using a backhoe/grab dredge commenced on the 17 th November 2009 in the Yarra River and Hobsons Bay and is scheduled to continue to mid 2010. Table A3.1 Field sampling dates and weather conditions (August – December 2009)

Progress Report Sampling Dates Weather Observations

5th August Moderate 10-15kt winds increasing to 15-20kts; waves 0.3-0.8m

11 th August Strong 20-25kt winds decreasing to 10-15kts; waves 0.6-1.5m

No.20 13 th August Light 5-10kt winds; waves 0.1-0.2m

15 th September Light 0-10kt winds; waves 0.1m

16 th September Moderate 10-15kt winds increasing to 15-20kts; waves 0.2-0.5m

No.21 18 th September Light 5-10kt winds increasing to 15-15kts; waves 0.2m

19 th October Light 0-10kt winds; waves 0-0.4m

21 st October Light 5-10kt winds increasing to 10-15kts; waves 0.4-0.5m

No.22 22 nd October Moderate 10-15kt winds increasing to 20kts; waves 0.3-0.4m

10 th November Light 0-10kt winds; waves 0-0.2m

11 th November Light 0-10kt winds; waves 0.1-0.3m

No.23 12 th November Light 5-10kt winds increasing to 15-20kts; waves 0.4m

7th December Light 0-5kt winds increasing to 10-15kts; waves 0.1-0.4m Moderate to strong 15-20kt winds decreasing to 0.-5kts; waves 9th December 0.5-0.6m

No.24 10 th December Moderate to strong 15-20kt winds; waves 0.5-0.6m

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 in 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 (August – December 2009) Report Number Exception Monitoring for August 2009 re-scheduled for the week beginning 4 th August, one ER090801 week prior to the planned commencement date to allow for weather and logistical constraints.

Table 7 (SEPP (WoV) Objectives and ANZECC trigger values) has been amended to ER090802 remove nutrient values and include ANZECC (2000) values for F7.

Dissolved Oxygen (DO) samples collected on 18/09/09 were not analysed by the ER090901 laboratory within the specified holding time.

Several total metal values for Patterson River and Dromana were incorrectly reported in Progress Report No. 1 (November 2007 to January 2008). ER091001 Several EWMA arsenic values for Patterson River and Dromana were incorrectly reported in Milestone Reports #1 and 2 and in Progress Report #3 for the Patterson River site only.

Monitoring for December 2009 was re-scheduled for the week beginning 7th ER091201 December, one week prior to the planned commencement date.

Results from Progress Reports

This subsection presents and discusses the data collected from field sampling events carried out from August to December 2009, as outlined in Progress Reports # 20 -2416 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.

16 EPA 2009. Baywide Water Quality Monitoring Program Progress Reports No 20 -24, August – December 2009.

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 and A3.4 summarise 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) 17

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

Table A3.3 Summary of exceedence of control limits for physico-chemical data and nutrients (August – December 2009)

Secchi disc Date Site Depth depth Ammonium Nitrate plus Nitrite Chlorophyll-a Total Nitrogen (m) (m) (µg/L) (µg/L) (µg/L) µg/L Measured Value EWMA Value EWMA Value EWMA Value EWMA 05/08/2009 Yarra River at Newport 0.5 1.3 53.2 05/08/2009 Corio Bay 0.5 2.3 13/08/2009 Dromana 0.5 5.7 11/08/2009 Middle Ground Shelf 0.5 2.4 0.84 16/09/2009 Yarra River at Newport 0.5 0.9 69.7 285 15/09/2009 Central Bay 0.5 16.4 4.9 18/09/2009 Dromana 0.5 5.6 6.4 19/10/2009 Yarra River at Newport 0.5 1.2 245.2 104.8 506 329 19/10/2009 Central Bay 0.5 4.3 22/10/2009 Dromana 0.5 5.2 19/10/2009 Patterson River 0.5 2.9 10/11/2009 Yarra River at Newport 0.5 1.7 84.2 297 12/11/2009 Central Bay 0.5 3.7 11/11/2009 Dromana 0.5 5.2 09/12/2009 Yarra River at Newport 0.5 1.2 94.7 8.16 1 3.11 553 348 07/12/2009 Patterson River 0.5 2.88 1

Notes 1. The chlorophyll a value is above the 90 th 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 above SEPP objectives where a Shewhart limit is not available. See Table A1.1 for detail.

Table A3.4 Summary of exceedence of control limits for metals (August – December 2009)

Date Site Depth Chromium Copper Zinc Mercury

(m) (µg/L) (µg/L) (µg/L) (ug/L) 05/08/2009 Yarra River at Newport - dissolved 0.5 8 13/08/2009 Dromana - dissolved 0.5 2 16/09/2009 Yarra River at Newport - total 0.5 0.7 16/09/2009 Corio Bay - total 0.5 15 10/11/2009 Yarra River at Newport - total 0.5 0.1 10/11/2009 Yarra River at Newport - dissolved 0.5 0.1 12/11/2009 Central Bay - dissolved 0.5 0.1 10/11/2009 PoM DMG - dissolved 0.5 0.1 10/11/2009 Patterson River - dissolved 0.5 0.1 11/11/2009 Dromana - dissolved 0.5 0.1 11/11/2009 Middle Ground Shelf - dissolved 0.5 0.1 11/11/2009 Sorrento Bank - dissolved 0.5 0.1 11/11/2009 Popes Eye -dissolved 0.5 0.1 09/12/2009 Yarra River at Newport - total 0.5 20 09/12/2009 Yarra River at Newport - dissolved 0.5 17

Notes

Yellow coloured cells indicate measured results above the Shewhart control limit (for ‘total’ fraction). See Table A2.3 for detail. Blue coloured cells indicate results above SEPP objectives for total metals where a Shewhart limit is not available See Table A1.1 for detail. Green coloured cells indicate results above ANZECC trigger values for dissolved metals (for metals, ANZECC triggers are the default objective when no SEPP value is specified) See Table A1.1 for detail.

Meteorological conditions

Rainfall Compared to the previous reporting period, there has been an increase in the amount of rainfall in the catchment surrounding PPB. Average rainfall levels have been recorded during the last six months (July – December 2009) compared to below average for the first six months of 2009 (Figure A3.1)

Figure A3.1 2009 Victorian rainfall deciles January – June 2009 and July – December 2009

The majority of nutrients and toxicants supplied by rivers to PPB are discharged during storms. 18 There were two storm events for the Yarra River identified in the last five months, on 26 th September and 22 nd November 2009, using storm event criteria outlined in Gibbs et al (2007) 19 (Figure A3.2). The storm event criteria for the Yarra River is that 24-hour rainfall must exceed 20 mm with rainfall continuing and Yarra River flow exceeds 15 m3.s-1 (~ 1,300 ML d-1) and is rising. The storm event criterion of 24-hour rainfall exceeding 16mm for Patterson River was reached on the 22 nd September, 31 st October and 22 nd November (Figure A3.3). No water quality sampling events coincided directly with the storm events. 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. Fairfield (river flow) and Viewbank (rainfall) were identified in Gibbs et al (2007) as the most relevant Melbourne Water (MW) 20 and Bureau of Meteorology (BoM) 21 sites for the Yarra River, while Moorabbin was identified as the most relevant BoM rainfall site for Patterson River.

18 Harris et al 1996, Port Phillip Bay Environmental Study Final Report 19 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. 20 All river flow data obtained from Melbourne Water < www.melbournewater.com.au > 21 All rainfall data obtained from the Bureau of Meteorology < www.bom.gov.au >

Figure A3.2 Yarra River rainfall, river flow and storm events August – December 2009

Figure A3.3 Patterson River rainfall and storm events August – December 2009

The Yarra River flow showed an accumulative lag following the September and smaller October rain event indicating that the rainfall was over a broader catchment area, discharging into PPB after the rain event had ceased. In contrast the trend in November river flow mimicked the rainfall suggesting a more localised catchment rainfall (Figure A3.2 and Figure A3.4). Figure A3.4 Victorian rainfall totals for August - December 2009

The November rain event was detected most clearly by the IMOS shipborne data. Data collected while the ship was moored at Port Melbourne shows a peak in turbidity levels, decreased salinity and increased chlorophyll fluorescence on the November 22 when rainfall was greatest. This was followed a few days later by a very large peak in chlorophyll fluorescence associated with river flows (Figure A3.5). The IMOS

shiptrack data also shows the extent to which the Yarra River flows are penetrating into PPB (Figure A3.6). Turbidity levels were highest on, and extended further into PPB on November 22. Lower salinity levels were recorded further into PPB several days after the flow event as were higher chlorophyll fluorescence.

Figure A3.5 IMOS shipborne data from Port Melbourne (November – December 2009)

Figure A3.6 IMOS shipborne track data (November 21 - 26 2009)

Physico-chemical data Salinity and Temperature

Salinity and temperature readings from both the EPA water quality and DPI nutrient cycling monitoring programs show similar patterns at each of the common sampling sites (Central Bay, Long Reef, Hobsons Bay and Middle Ground Shelf). Water temperature showed a sharp increase between the October and November water quality sampling events with the DPI data showing the sharpest increase occurring from 7 th – 10 th November. This coincides with a period of higher air temperatures and increased sun hours (Figure A3.7). Figure A3.7 Surface water temperature at Hobsons Bay (August – December 2009)

25 40

20 C) o C) o

20 Sunhours

15 Air temperature ( Watertemperature (

10 0 06-07-09 26-07-09 15-08-09 04-09-09 24-09-09 14-10-09 03-11-09 23-11-09 13-12-09 02-01-10 22-01-10 Date

EPA water quality data (probe) EPA water quality data (CTD) DPI nutrient cycling data Viewbank air temperature Melbourne sun hours Differences were observed in surface and bottom water temperatures at several sites. This is consistent with local heating of surface waters. The DPI data shows evidence of mixing of surface and bottom waters bringing temperatures closer together (Figure A3.8). Figure A3.8 Central Bay surface and bottom water temperature (August – December 2009)

18 C) o

16 Temperature ( Temperature

10 26-07-09 15-08-09 04-09-09 24-09-09 14-10-09 03-11-09 23-11-09 13-12-09 02-01-10 Date

DPI nutrient cycling data - surface temperature DPI nutrient cycling data - bottom temperature EPA water quality data - surface temperature EPA water quality data - bottom temperature

Temperature profiles from the monthly sampling and the IMOS shipborne data show water temperatures in late 2009 are warmer than during the same period in 2008 (Figure A3.9), and detect a Baywide acceleration of warming associated with the hot spell in early November 2009.

Figure A3.9 IMOS shipborne water temperature measurements for PPB (September – December 2008 and 2009)

Salinity measurements in PPB are inversely related to freshwater inputs. A comparison of rainfall and salinity data from 1986 – 2009 is presented in Figure A3.10 showing that lower salinity levels are associated with higher rainfall. The data indicates that since the beginning of drought conditions in 1998, bay salinity has been higher than adjacent Bass Strait salinity (~35.5psu).

Figure A3.10 Annual rainfall and average salinity measurements for PPB (1986 – 2009) 22

40 1000

900

800

700

35 600 Average rainfall 1986-2009 rainfall (mm) rainfall salinity (mg/L) salinity 500

400

300

30 200 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 Year salinity total rainfall

22 All rainfall data obtained from the Bureau of Meteorology < www.bom.gov.au >

A declining trend in salinity was seen throughout the bay during this reporting period. The bay is still hypersaline, however the return of average rainfall during this period has resulted in salinity readings decreasing by around 0.5psu leading to the lowest average salinities seen in PPB since the commencement of the program (Figure A3.11).

Figure A3.11 Average salinity for PPB (November 2007 – December 2009)

38.0

37.5

37.0

36.5

36.0 Salinity (psu)

35.5

35.0

34.5 Oct-07 Jan-08 Apr-08 Jul-08 Nov-08 Feb-09 May-09 Sep-09 Dec-09 Date

Average salinity all sites Average salinity excl. Yarra River at Newport

The drop in salinity levels has also influenced dissolved oxygen (DO) measurements at some sites. The DPI nutrient cycling data shows higher dissolved oxygen (% saturation) corresponding to lower salinity (Figure A3.12).

Figure A3.12 Central Bay surface salinity and dissolved oxygen measurements (August - December 2009)

110 37.4

105 37.2

100 37 %Saturation 95 36.8 Salinity(psu)

90 36.6

85 36.4 26-07-09 15-08-09 04-09-09 24-09-09 14-10-09 03-11-09 23-11-09 13-12-09 Date DPI nutrient cycling data - DO DPI nutrient cycling data - salinity

The influence of rainfall and associated river flow on salinity is most evident at the Yarra River at Newport site. Surface salinity measurements have been less than 34.2psu since August 2009. CTD profiles show the greater influence of freshwater in surface waters in 2009 when compared to the same period in 2008 (Figure A3.13). Figure A3.13 Salinity CTD profiles for the Yarra River at Newport (August – December 2008 and 2009)

Salinity (psu) 20 22 24 26 28 30 32 34 36 38 0

8 Depth (m) Depth

12 Aug-08 Sep-08 Oct-08 Nov-08 Dec-08

Aug-09 Sep-09 Oct-09 Nov-09 Dec-09 14

The IMOS shipborne data also shows the increased flows from the Yarra River as reflected in the lower salinities. The increase in fresh water into PPB has eroded the salinity throughout PPB as seen in late November / early December 2009 with the 36.5psu contour extending ~30km further south into PPB by the Yarra River plume (Figure A3.14). Comparison of late 2008 and late 2009 salinity data show that flow events observed in the late 2008 period were confined in Hobsons Bay rather than dispersing through the bay (as seen in the late 2009 data). The dispersion of lower salinity into the bay tags the momentum of the enhanced Yarra River flow. This identifies a transport pathway for water quality parameters sourced from the Yarra catchment.

Figure A3.14 IMOS shipborne salinity measurements for PPB (September – December 2008 and 2009)

Stratification The Detailed Design states that stratification is deemed to occur where there is a difference of >10psu in salinity or the temperature differs by more than 0.5°C between surface and bottom waters. 23 During this reporting period there was only one occasion where both salinity and temperature stratification were observed simultaneously. This was at the Yarra River at Newport in October (Figure A3.15). This is expected when the stratification is a result of warmer fresh water overlying more saline water 24 as seen at the Yarra River following rainfall and associated high river flow.

23 PoMC 2010. Water Quality – Detailed Design CDP_ENV_MD_023 Rev 4.0 Port of Melbourne Corporation. 24 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.

Figure A3.15 Yarra River at Newport temperature and salinity stratification (October 2009)

Temperature (oC) 13.5 14 14.5 15 15.5 16 16.5 17 0 20

1 23

2 26

3 29 Salinity Depth (m) 4 32 temperature-depth 5 35 temperature-salinity

6 38

Temperature stratification was also observed at numerous other sites across PPB throughout the reporting period as shown in Table A3.5. This appears to be correlated with salinity (ie. freshwater inflows overlying saline bay waters) at Yarra River at Newport, Hobsons Bay and Long Reef while at other sites it is more likely a result of thermal heating. The strongest temperature stratification occurred in November 2009 where there was ~3.5°C difference between the surface and bottom water at Hobsons Bay, Central Bay and PoM DMG (Figure A3.16). Temperature stratification in PPB is most common from August – February occurring in low wind conditions when the air temperature exceeds water temperature. 25 Figure A3.16 Temperature profiles from Hobsons Bay, Central Bay and PoM DMG (November 2009)

Temperature ( oC) 15 16 17 18 19 20 21 22 23 24 25 0

Depth Depth (m) 15

Hobsons Bay Central Bay PoM DMG

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

Table A3.5 Temperature stratification in PPB (August – December 2009) Site Temperature Salinity Month Site Name Location Difference Difference Aug-09 Yarra River at Newport Inshore 0.7 -4.8 Yarra River at Newport Inshore 1.4 -5.2 Hobsons Bay Inshore 0.5 -1.3 Dromana Inshore 0.5 0.0 Sep-09 Long Reef Inshore 0.9 -0.4 PoM DMG Central 0.7 0.0 Central Bay Central 1.1 -0.1 Yarra River at Newport Inshore 2.6 -14.2 Oct-09 Hobsons Bay Inshore 0.8 -0.2 PoM DMG Central 0.6 0.0 Yarra River at Newport Inshore 1.7 -1.1 Hobsons Bay Inshore 3.5 -0.8 Dromana Inshore 0.8 0.0 Nov-09 Patterson River Inshore 1.0 0.0 PoM DMG Central 3.6 0.0 Central Bay Central 3.6 0.0 Yarra River at Newport Inshore 1.3 -8.1 Dec-09 Hobsons Bay Inshore 0.6 -1.3 Central Bay Central 0.5 0.0

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.26 There were no observed exceedences of DO for the WQBMP. Results from the DPI Nutrient Cycling Baywide Monitoring Program show the variability that can occur in DO readings that is not evident in single samples collected for the WQBMP (Figure A3.17).

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

Figure A3.17 Hobsons Bay dissolved oxygen measurements (August – December 2009)

115

110

105

100

90 % % saturation

70 26-07-09 15-08-09 04-09-09 24-09-09 14-10-09 03-11-09 23-11-09 13-12-09 02-01-10 Date

DPI nutrient cycling data - surface DPI nutrient cycling data - bottom EPA water quality data (lab) EPA water quality data (CTD)

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 was generally good across the bay with the SEPP objectives met at most sites. The exceptions included the Yarra River at Newport and Patterson River (Table A3.3). Water clarity at the Yarra River at Newport site did not meet the SEPP objective of >2m during each of the last 5 months, continuing the trend seen throughout most of the program (Figure A3.18). As predicted by the SEES, dredging activities are likely to have influenced water clarity at this site throughout the CDP. More recently, the increase in rainfall and associated river flow has affected water clarity with the Yarra River one of the major sources of particulates and suspended solids entering into PPB. 27 The limited historical data for Secchi depth from the Yarra River indicates that there are periods of low water clarity experienced at this site in the absence of dredging (Figure A3.19).

27 SKM 2007 Head Technical Report Water Quality , Port Phillip Bay, Channel Deepening Project Supplementary Environmental Effects Statement, Technical Appendix 39

Figure A3.18 Water clarity (Secchi depth) at Yarra River at Newport (November 2007 – December 2009

Figure A3.19 Historical and current Secchi depth data for the Yarra River (December 2004 – December 2009)

3.5

2.5

SEPP >2m 2

1.5 Secchi Secchi disc (m) depth 1

0.5

0 Jul-09 Jul-06 Oct-09 Oct-06 Apr-07 Jan-10 Jan-07 Jun-08 Mar-09 Mar-06 Feb-08 Feb-05 Nov-07 Nov-04 Sep-08 Dec-08 Aug-07 Sep-05 Dec-05 May-05 Date Enesar 2004-05 DPI 2006-07 EPA 2007-09

Water clarity at Patterson River in October (2.9m) did not meet the SEPP objective of >3m. This may have been influenced by rainfall in the week prior to the sampling event (Figure A3.3).

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 5 months (Figure A3.20). The annual median (5.8 NTU) and annual 90 th percentile (15.3 NTU) for the last 12 months of monitoring were well below the SEPP objectives of <20NTU and <50 NTU respectively (Table A6.1). Figure A3.20 Yarra River at Newport CTD turbidity profile August – December 2009

Turbidity (NTU) 0 2 4 6 8 10 0

Depth (m) 8 Aug-09

Sep-09 10 Oct-09

Nov-09 12 Dec-09

The IMOS shipborne turbidity data for the period September – December 2009 is shown in Figure A3.21 and compared against measurements taken for the same period in 2008. Higher turbidity levels (3-4NTU) associated with TSHD dredging were evident in September, October and December 2008 compared to periods when dredging was either minor (grab/backhoe dredge) or absent such as in November 2008 and late 2009 (Figure A3.21). Short-term periods of elevated turbidity measuring 10-40 NTU were evident during the late 2008 period within Hobsons Bay, with the most extensive plume associated with enhanced Yarra River flow in late November 2008. In contrast, the short-term peaks in turbidity in Hobsons Bay during late 2009 were lower, measuring 5-10 NTU, which also coincided with Yarra River flows.

Figure A3.21 IMOS shipborne turbidity measurements for PPB (September to December 2008 and 2009)

Total suspended solids (TSS) TSS concentrations have closely followed the pattern of Secchi depth at the Yarra River at Newport site since the commencement of the WQBMP in November 2007 (Figure A3.22). Unlike Secchi depth, the TSS SEPP F7 objectives for Yarra River at Newport were met with the median (9.6mg/L) and 90 th percentile (24.9mg/L) below the SEPP objectives of < 25 mg L -1 and < 60 mg L 1 respectively (Table A6.1). Figure A3.22 Secchi depth and TSS at Yarra River at Newport (November 2007 – December 2009)

0 35

0.5 30

1 25

1.5 20 2 15 2.5

Secchi disc depth (m) disc depth Secchi 10 3 Total suspended solids (mg/L) solids suspended Total

3.5 5

4 0 Jul-09 Jul-08 Apr-09 Oct-09 Apr-08 Oct-08 Oct-07 Jan-10 Jan-09 Jun-09 Jan-08 Jun-08 Feb-09 Mar-09 Feb-08 Mar-08 Nov-09 Nov-08 Nov-07 Dec-09 Dec-08 Aug-09 Sep-09 Dec-07 Aug-08 Sep-08 Sep-07 May-09 May-08 Month Secchi disc depth Total suspended solids

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. 28 Nutrient discharges are deemed to be acceptable if they do not cause chlorophyll-a objectives to be breached. The expected variation in water quality in PPB is most effectively expressed via the control limits.

Ammonium

During the current reporting period all sites, with the exception of Dromana, showed levels of ammonium to be similar to the historical mean and below Shewhart and EWMA control limits. Highest ammonium concentrations were found in the north of the bay at the Yarra River at Newport and in the west at Long Reef.

EWMA values at Dromana have exceeded the control limit of 5 µg/L since the commencement of the program. December 2009 was the first month that the EWMA value dropped below the control limit (Figure A3.23). Ammonium levels at Dromana have shown a decreasing trend since March 2009 (Figure A3.24) with concentrations moving closer to the historical mean value.

Figure A3.23 Ammonium EWMA control chart for Dromana (November 2007 – December 2009)

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

Figure A3.24 Ammonium Shewhart control chart for Dromana (November 2007 – December 2009)

Nitrate plus Nitrite

Levels of nitrate plus nitrite (NOx or ‘oxidised nitrogen’) within PPB (excluding Yarra River at Newport) are generally similar to the historical mean. At the southern PPB sites there is evidence of seasonal peaks of NOx during winter corresponding with lower water temperature and salinity. These seasonal peaks in NOx levels are not an isolated event with similar peaks of varying magnitude observed in 1994, 2006, 2007 and 2008 29 . The winter peaks at Middle Ground Shelf (MGS) in 2008 and 2009 influenced the EWMA for several months (Figure A3.25)

Figure A3.25 NOx EWMA control chart for MGS (November 2007 – December 2009)

29 EPA 2009 Filenote Review of nitrogen levels in the south of PPB

Prior to July 2009, NOx levels in Corio Bay were showing an underlying increasing trend in the raw (uncensored) values. This has since changed, with data from the last six months showing NOx levels closer to the historical mean (Figure A3.26 and Figure A3.27).

Figure A3.26 NOx EWMA control chart for Corio Bay (November 2007 – December 2009)

Figure A3.27 NOx Shewhart control chart for Corio Bay (November 2007 – December 2009)

A single short term Shewhart exceedence was seen at Central Bay in September which influenced the EWMA value for several months (Figure A3.28 and Figure A3.29)

Figure A3.28 NOx Shewhart control chart for Central Bay (November 2007 – December 2009)

Figure A3.29 NOx EWMA control chart for Central Bay (November 2007 – December 2009)

NOx levels at the Yarra River at Newport site have been reasonably high during this reporting period (excluding November), with the first Shewhart exceedence in October 2009 (Figure A3.30). The EWMA control limit of 39.52ug/L has been exceeded each month for the last 6 months (Figure A3.31). This increase in NOx levels corresponds to a period of increased rainfall and river flow from the Yarra River. Figure A3.30 NOx Shewhart control chart for Yarra River at Newport (November 2007 – December 2009)

Figure A3.31 NOx EWMA control chart for Yarra River at Newport (November 2007 – December 2009)

Total Nitrogen

The results for total nitrogen at all sites were generally similar to the historical mean and below the Shewhart and EWMA control limits.

As observed with NOx during the last 6 months, increased levels of total nitrogen have been seen at the Yarra River at Newport site. The Shewhart control limit was exceeded in October and December 2009 (Figure A3.32) and the EWMA control limit was exceeded in the last four months (Figure A3.33). Figure A3.32 Total nitrogen Shewhart control chart for Yarra River at Newport (November 2007 – December 2009)

Figure A3.33 Total nitrogen EWMA control chart for Yarra River at Newport (November 2007 – December 2009)

Phosphate

All results for phosphate were below the Shewhart control limits and generally below the historical mean. Phosphate EWMA values are showing a downward trend at all sites. The decline is not a recent phenomenon. The mean phosphate concentration at the Central Bay site declined from 70 µg/L in 1984-99 to 60 µg/L in 2001-06, dropping to 43 µg/L in 2008-09.

Hobsons Bay results are presented with other sites showing a similar general trend (Figure A3.34 and Figure A3.35). Figure A3.34 Phosphate Shewhart control chart for Hobsons Bay (November 2007 – December 2009)

Figure A3.35 Phosphate EWMA control chart for Hobsons Bay (November 2007 – December 2009)

Total Phosphorous

The concentrations of total phosphorous are generally below the historical mean and below the Shewhart and EWMA control limits at all sites. Similar to phosphate the EWMA values for total phosphorous are also showing a downward trend.

Port of Melbourne Dredge Material Ground (PoM DMG) results are presented with other sites showing a similar general trend (Figure A3.36 and Figure A3.37).

Figure A3.36 Total Phosphorous Shewhart control chart for PoM DMG (November 2007 – December 2009)

Figure A3.37 Total Phosphorous EWMA control chart for PoM DMG (November 2007 – December 2009)

Silicate There are no control limits or SEPP objectives for silicate. Highest silicate concentrations were reported at the Yarra River at Newport site. Peaks in silicate were observed in September, October and December 2009 at the Yarra River at Newport (Figure A3.38) and at Patterson River in December 2009 (Figure A3.39).

Figure A3.38 Silicate control chart for Yarra River at Newport (November 2007 – December 2009)

Figure A3.39 Silicate control chart for Patterson River (November 2007 – December 2009)

Phytoplankton and Algal Pigments Phytoplankton activity is measured through cell counts, chlorophyll-a measurements and in-situ chlorophyll fluorescence. Total phytoplankton cell numbers remained low for most of the reporting period followed by a dramatic increase during November 2009 at the Yarra River at Newport and Hobsons Bay sites. This was followed by a further increase in total phytoplankton numbers at Hobsons Bay and an increase in cell numbers at Patterson River which may have been a result of the phytoplankton moving further into the bay or a separate population. The phytoplankton cell numbers in November and December 2009 are the highest seen during the WQBMP (Figure A3.40). Rapid increases in phytoplankton cell numbers, usually dominated by a single species, are called a bloom. 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. 30 The phytoplankton “bloom” seen in November and December was made up primarily of the diatom Skeletonema japonicum / psuedeocostatum . This “bloom” in phytoplankton was preceded by increased rainfall and sustained river flows from the Yarra River in late September and October (Figure A3.2). This influx of freshwater carried increased nutrient loads into PPB with peaks in nitrogenous compounds and silicate observed in October 2009 at the Yarra River at Newport site. Nutrient concentrations then dropped considerably in November following uptake by phytoplankton (Figure A3.41). The combination of increased nutrients, decreased salinity and a rise in water temperature all contributed to the increased phytoplankton productivity and biomass in November and December 2009.

Figure A3.40 Total phytoplankton cell numbers across PPB (February 2008 – December 2009)

12000000

10000000

8000000

6000000

4000000 Total # phytoplankton cells # phytoplankton Total

2000000

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

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

30 Elias et al. 2004 Port Philip Bay Channel Deepening Project Environmental Effects Statement – Marine Ecology Specialist Studies, Volume 8 Plankton and Nekton studies .

Figure A3.41 Phytoplankton and nutrient levels at the Yarra River at Newport (January - December 2009)

12000000 1200

10000000 1000

8000000 800

6000000 600 Nutrients(ug/L)

#phytoplankton cells 4000000 400

2000000 200

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

S.japonicum Total phytoplankton Organic N NOx Total N Silicate

A smaller peak in phytoplankton biomass was captured by the DPI nutrient cycling monitoring program in September. Data from Hobsons Bay and Long Reef both showed an increase of in-situ chlorophyll fluorescence in September 2009 associated with the rain event which was not captured by the EPA monthly data (Figure A3.42). Figure A3.42 Hobsons Bay surface Chlorophyll-a measurements (August – December 2009)

25 50

20 40 C) o 15 30 Chlorophyll-a 10 20 (mm) Rainfall Water temperature ( temperature Water

5 10

0 0 06-07-09 26-07-09 15-08-09 04-09-09 24-09-09 14-10-09 03-11-09 23-11-09 13-12-09 02-01-10 22-01-10 Date

DPI nutrient cycling data - water temperature DPI nutrient cycling data - chlorophyll-a EPA water quality data - chlorophyll-a Yarra Rainfall

In-situ chlorophyll fluorescence data collected through IMOS shows more phytoplankton activity in late 2009 associated with the Yarra River plume when compared to the same period in late 2008 (Figure A3.43). Both the late 2008 and late 2009 records detect seasonal plankton activity in September occurring both inside the bay and in Bass Strait waters. By December the blooms are only expressed within the bay and relate more closely to Yarra river discharge patterns. The sustained Yarra River flows in 2009 coincided with prevailing plankton activity in the daily IMOS shipborne observations. Figure A3.43 IMOS shipborne in-situ chlorophyll fluorescence measurements for PPB (September – December 2008 and 2009)

Chlorophyll -a concentrations reflect the increased phytoplankton biomass seen in PPB in December 2009. Figure A3.44 provides a general view of the spatial variation seen in chlorophyll-a concentrations during the previous twelve months using data interpolated with the Spline method. 31

31 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 11 sites over a number of days each month and does not account for minor temporal changes caused by environmental factors.

Figure A3.44 Interpolated chlorophyll-a data (January – December 2009)

The phytoplankton counts from the Yarra River at Newport did not correspond with the chlorophyll-a data in November and December 2009 (Table A3.6). The peak in chlorophyll -a in December corresponded with average cell numbers, and lagged behind a peak in cell numbers in November (Figure A3.45).

Table A3.6 Phytoplankton, chlorophyll-a and chlorophyll fluorescence at the Yarra River at Newport (November – December 2009) November 09 December 09 Total phytoplankton 11 380 250 3 300 000 Chlorophyll-a 2.40 8.16 Fluorescence - surface 0.94 1.43 Fluorescence - bottom 1.45 0.56

Figure A3.45 Total phytoplankton cell count and chlorophyll-a concentrations at the Yarra River at Newport site (November 2007 – December 2009)

12000000 9

8 10000000 7

8000000 6

5 6000000 4

4000000 3 Chlorophyll-a (ug/L)

2 Total phytoplankton (cells/L) Total phytoplankton 2000000 1

0 0 Jul-08 Jul-09 Apr-08 Apr-09 Oct-08 Oct-09 Jun-08 Jan-08 Jun-09 Jan-09 Mar-08 Mar-09 Feb-08 Feb-09 Nov-07 Nov-08 Nov-09 Aug-08 Sep-08 Dec-07 Aug-09 Sep-09 Dec-08 Dec-09 May-08 May-09 Month

Total phytoplankton Chlorophyll-a

Species richness (number of taxa) during the period August – December 2009 varied considerably across sites and sampling events. Total number of taxa ranged from a low of 27 at Patterson River (November) to a high of 51 at Sorrento (October) and Pope’s Eye (November). Mean number of taxa recorded was highest at Popes Eye (43.6) and lowest at Long Reef (35.8). This is exactly the opposite of the previous reporting period (February to July 2009); when these figures were reversed. The pattern of species richness mirrors that of phytoplankton abundance, with greatest species richness recorded during times of lowest abundance (Figure A3.46).

Figure A3.46 Number of taxa recorded at Long Reef and Popes Eye (January to December 2009)

35 No. of of taxa No.

20 Jan-09 Feb-09 Mar-09 Apr-09 May-09 Jun-09 Jul-09 Aug-09 Sep-09 Oct-09 Nov-09 Dec-09 Month

Long Reef Popes Eye

Metals Many of the metal samples were below the detection limit. There were only a small number of reported exceedences above control limits for total and dissolved metals. Table A3.4 provides a summary of all control limit exceedences, including SEPP (WoV) and ANZECC, where no Shewhart are available. Summary statistics for metals have been calculated for comparison against SEPP objectives. Regionally specific SEPP objectives apply to total metals. Where there is no regionally specific objective in SEPP, the SEPP (ANZECC) objective is applied to dissolved metals (Appendix 6). Summary statistics are calculated using the last 12 months of data (January - December 2009) and include the mean, median, 90 th percentile, minimum and maximum value. SEPP (WoV) objectives for metals are based on maximum values.

Arsenic During the current reporting period total arsenic concentrations across PPB were all below the Shewhart and EWMA control limits (where available). For each of the sites where an EWMA control limit is available, there was a decreasing trend in EWMA values. Central Bay results are presented with other sites showing a similar general trend (Figure A3.47 and Figure A3.48). Arsenic values from Corio Bay are showing a slight seasonal pattern with peaks in summer/ autumn (Figure A3.49).

Figure A3.47 Arsenic Shewhart control chart for Central Bay (November 2007 – December 2009)

Figure A3.48 Arsenic EWMA control chart for Central Bay (November 2007 – December 2009)

Figure A3.49 Arsenic Shewhart control chart for Corio Bay (November 2007 – December 2009)

A comparison of the WQBMP data against the Beach monitoring program data and Melbourne Water monitoring data is presented in Figure A3.50. Seasonal variations are evident in EPA WQBMP and Beach monitoring data. The Melbourne water monitoring data shows that arsenic concentrations within the Yarra and Maribyrnong Rivers are of the same relative order as PPB, although there is no evidence of seasonal variations consistent with that recorded in PPB waters Summary statistics based on the last 12 months of data show the SEPP F6 objective of <3µgL/L was not met at the Yarra River at Newport, Hobsons Bay, Corio Bay or Middle Ground Shelf (Appendix 6). There were no SEPP (WoV) exceedences during the current reporting period. 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 32 .

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

Figure A3.50 Comparison of arsenic data from the Melbourne Water, EPA Beach and Water Quality monitoring programs (January – December 2009)

4.5

3.5

2.5

Arsenic Arsenic (ug/L) 2

1.5

0.5

0 17/01/2009 8/03/2009 27/04/2009 16/06/2009 5/08/2009 24/09/2009 13/11/2009 2/01/2010 Date

MW_Yarra R MW_Maribrynong R WQ_Yarra River at Newport WQ_Hobsons Bay Beach_Elwood Beach_Middle Park Beach_Port Melbourne Beach_Sandridge Beach_St Kilda Beach_Williamstown

Cadmium

All samples in the current reporting period were below the limit of reporting (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 <0.15µg/L (which is below the LOR) was not met at Patterson River and all sites in the F6 general segment due the detection of cadmium at the LOR (0.2 µg L-1) in June 2009 (Appendix 6).

Chromium The majority of chromium results during the current reporting period were below the LOR (0.5 µg/L) and within both control limits and SEPP objectives. The exception was a Shewhart exceedence of total chromium at Yarra River at Newport in September (Figure A3.51). The SEPP (WoV) F6 objective of <5µg/L for total chromium was met at all sites (Appendix 6).

Figure A3.51 Total chromium Shewhart control chart for Yarra River at Newport (November 2007 – December 2009)

Copper

The majority of copper results were below the LOR (1 µg/L) and within both control limits and SEPP objectives. The exception included a SEPP (ANZECC) exceedence of dissolved copper at Dromana in August 2009. The SEPP (ANZECC) F6 objective of <0.3 µg/L was met at all other sites (Appendix 6).

Lead The results for lead were generally below the LOR (0.2 µg/L) and/or within both control limits and SEPP (WoV) objectives (Appendix 6).

Mercury Mercury results were generally below the LOR (0.1 µg/L) except during November 2009 when all mercury results were reported at the LOR. The Shewhart limit (0.1 µg/L) and SEPP (WoV) F7 objective (0.05 µg/L) for total mercury at Yarra River at Newport was exceeded in November 2009 as was the SEPP (ANZECC) F6 objective for all sites within the inshore and general segments (Appendix 6).

Nickel The results for nickel were generally below the LOR and/or within both control limits and well below the SEPP (WoV) objectives (Appendix 6).

Zinc

The majority of zinc results were below the LOR (5 µg/L) and within derived control limits. The exceptions included Corio Bay and the Yarra River at Newport. Metal concentrations in PPB are generally low but can be affected by environmental conditions, particularly catchment run-off associated with rainfall. 33 During this reporting period a single SEPP (WoV) exceedence of

33 EPA 2009. Extended Monitoring of Beach Water Quality in Port Philip Bay – March 2008 – September 2009.

total zinc was observed at Corio Bay in September 2009 with the corresponding dissolved (bio-available) component below the LOR (Table A3.4). Peaks in zinc concentrations were also observed at the Yarra River at Newport with SEPP (ANZECC) exceedences of dissolved zinc in August and December (Figure A3.52) and a Shewhart exceedence of total zinc in December 2009 (Figure A3.53). Comparison against the Beach monitoring program data and Melbourne Water monitoring data show that higher zinc levels in PPB do correspond to higher levels recorded in the Yarra River (Figure A3.54).

Figure A3.52 Dissolved zinc control chart for Yarra River at Newport (November 2007 – December 2009)

Figure A3.53 Total zinc Shewhart control chart for Yarra River at Newport (November 2007 – December 2009)

Figure A3.54 Comparison of zinc data from the Melbourne Water, EPA Beach and Water Quality monitoring programs (January – December 2009)

160 70

140 60

120 50

100 40

30 MW MW Zinc(ug/L) 60 WQ and Beach Zinc andWQ Beach (ug/L)

20 40

10 20

0 0 17/01/2009 8/03/2009 27/04/2009 16/06/2009 5/08/2009 24/09/2009 13/11/2009 2/01/2010 Date

MW_Yarra R MW_Maribrynong R WQ_Yarra River at Newport WQ_Hobsons Bay Beach_Elwood Beach_Middle Park Beach_Port Melbourne Beach_Sandridge Beach_St Kilda Beach_Williamstown

Summary statistics based on the last 12 months of data show the SEPP (WoV) F6 objective was not met at all sites. In only two of these instances it was attributed to results from the current 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)

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 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.

Australian Laboratory Services (ALS) employs a QAQC program as follows: • 5% Method Blanks – one analysed within each process lot of 20 samples; • 10% Laboratory Duplicates – two analysed within each process lot of 20 samples; • 5% Laboratory Control Samples (LCS) – one analysed within each process lot of 20 samples; and • 5% Matrix Spikes (MS) – one analysed within each process lot of 20 samples.

Laboratory comparison on filtered and unfiltered nutrients

The current Baywide Monitoring Program measures filtered inorganic nutrients whereas historically, inorganic nutrients were measured using unfiltered samples. This inconsistency prompted an investigation of both filtered and unfiltered samples from the monthly monitoring program to determine the magnitude of difference between the filtered and unfiltered results and the impact of using control limits based on unfiltered data to assess filtered sample results. Differences in filtered and unfiltered results are expected as the total result is representative of both particulate (unfiltered) and dissolved (filtered) fractions. The results support previous findings that differences are minor for phosphate, ammonium and silicate. Unexpectedly, the results for filtered NOx, nitrite and nitrate

were generally higher than the corresponding unfiltered result. This was most likely due to low level contamination from the filters.

The impact of using Shewhart control limits based on unfiltered data to assess filtered sample results appears to be minor for all parameters with the exception of NOx. Ammonium and phosphate samples are similar enough that use of Shewhart control limits based on unfiltered values appears to be adequate for assessing filtered samples, especially if prediction limits are included. Comparisons of the prediction intervals to the Shewhart control limits for NOx appears to result in inconclusive results. The nature of the discrepancy for NOx is likely to result in occasional false positives (i.e. an exceedence will be reported when the result is not truly outside natural variability).

Changing procedure at this stage of the program will limit the use of data collected to date in the future. For continuity with the current program, EPA will continue analysing filtered samples. Analysis of both filtered and unfiltered samples for nitrate, nitrite and NOx will be undertaken due to the potential contamination of filtered samples.

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. Exceptions included: • Low levels of nitrates (at or just above the LOR) were detected in freshwater field blanks in September. This has been attributed to filtering cartridges and is not considered ecologically significant. • Moderate levels of nitrates (7.2-9.1µg/L) were detected in two of the three freshwater field blanks in October. The results for seawater samples were considered to be valid with contamination by NOx evident in freshwater samples only. 34

Field replicate samples Metals samples for the period August – December 2009 showed some minor discrepancies between original and replicate results however all results were found to be within the measurement uncertainty (MU) provided by the laboratory. Nutrient replicate samples for the period August - December 2009 were generally found to be in agreement with the original value. Only three results were found to be outside of the MU provided by the laboratory (Table A4.1).

34 EPA 2009 October 09 QAQC Report

Table A4.1Nutrient replicate results outside of the laboratory MU (August – December 2009)

Nitrate plus Nitrate Nitrite 15/09/09 PoM DMG 4.1+/-0.7 4.5+/-0.6 15/09/09 North Replicate 14.6+/-2.5 15.0+/-1.9 9/12/09 Corio Bay 1.3+/-0.2 9/12/09 Southern Replicate 1.9+/-0.3

All data is QAQC checked as outlined in the QAQC SOP 35 prior to acceptance. The discrepancy in the replicate results from September 2009 was not identified during this QAQC process. This oversight led to a review of the QAQC SOP and a number of improvements implemented including the requirement for all data to be checked and then independently verified by a second person. Results for NOx at this site are consistently low (generally <5µg/L) and the original reported result is considered to be valid. The replicate results from December 2009 for NOx were only marginally different and were therefore accepted as valid data.

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.

35 EPA 2009 Standard Operating Procedure Laboratory Quality Assurance and Quality Control

APPENDIX 5 - RESULTS OUTSIDE OF NATURAL/EXPECTED VARIABILITY

As outlined in the Detailed Design ( Decision Framework for Management ) PoMC led an assessment of results flagged as outside of natural/expected variability. 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. b) If the results exceed control limits then they are deemed to be ‘outside of natural variability’. 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.

PoMC Assessment Multiple lines of evidence are considered to assess whether the results are outside of expected variability. All results up to December 2009 have been reviewed by the 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.

Table A5.1 PoMC Assessment (August - December 2009)

PARAMETER SITES EXCEEDENCE TYPE DATES ASSESSMENT OUTCOME

Capital or minor dredge works were being undertaken during or in the days prior to August - October 2009 sampling, decreasing water clarity at sites adjacent to dredging.

This exceedence is relatively small and may not be within the historical range due Yarra River at Newport November 2009 to the small historical dataset that does not adequately represent the historical Water Clarity conditions of the site. SEPP (Secchi depth) (Secchi Depth) This exceedence was most likely due to increase in rainfall and river flow during the December 2009 week of sampling. Surface runoff from rainfall increases particulate inputs into a river system thereby impacting visibility.

Reduced water clarity may have been due of poor weather conditions in the days Patterson River October 2009 prior to sampling.

The raw result was slightly above the long-term median/mean and above the historical range. Conditions were localised and the annual median and 90th Chlorophyll a Middle Ground Shelf EWMA August 2009 percentile results were below the SEPP objectives. The EWMA value was equal to the control limit in August and below the control limit the following month.

This result is not considered to be biologically significant as ammonium concentrations at Dromana have returned exceedences of the control limits since November 2007. These exceedences are thought to be associated with a baseline Ammonium Dromana EWMA August - November 2009 shift in concentrations since the 1990's. Furthermore, the control limit is low when compared to control limits from other sites, and is based on a small historical dataset.

The raw August 2009 result was below the Shewhart limit and within the historical Nitrate plus nitrite (NOx) Yarra River at Newport August 2009 range. A peak in raw NOx concentrations in July 2009 is having a sustained influence on the EWMA and is likely to continue to influence in coming months.

EWMA

This is the first occasion since the commencement of the Baywide Monitoring September - October 2009 Program that the Shewhart control limit has been exceeded with the result outside of the historical range. Control limits are based on a limited historical dataset (collected during sustained period of drought) that does not adequately represent the full range of within and between year variation that may occur at this site. Evidence suggests that these results are likely to be due to seasonal trends. On- going monthly monitoring results at this site will continue to be assessed to Shewhart October 2009 determine if there is a longer term shift in NOx and TN.

PARAMETER SITES EXCEEDENCE TYPE DATES ASSESSMENT OUTCOME

This exceedence was a result of elevated values reported in the previous months November 2009 as the November 2009 raw value was below the control limit.

EWMA The raw NOx value was outside of the historical range (based on a limited dataset) for this site. This exceedence is most likely a result of increased catchment inputs December 2009 into the Yarra River following rainfall. This pattern of exceedence is also reflected in the TN exceedences reported at this site.

NOx exceedences have been occurring since January 2009. Exceedences earlier this year were largely driven by an underlying increasing NOx trend. A peak in May Corio Bay EWMA August 2009 2009 has been having a sustained influence upon the EWMA with all subsequent raw results relatively low.

This is the first occasion since the commencement of the Baywide Monitoring Program that the Shewhart control limit has been exceeded and the raw result is Shewhart September 2009 outside of the historical range. As the October 2009 result was relatively low, the September 2009 value is considered to be transient and resulted in a short-term exceedence of the control limit.

Central Bay These are the first occasions since the commencement of the Baywide Monitoring Program that the EWMA control limit has been exceeded. A peak in raw NOx September - October 2009 concentrations in September 2009 is having a sustained influence on the EWMA and is likely to continue to influence in coming months. EWMA

This exceedence was a result of elevated values reported in the previous months November 2009 as the November raw value was below the control limit and no exceedence was reported in December 2009.

A peak in raw NOx concentrations in June 2009 is having a sustained influence on the EWMA. The exceedence is limited to this site. The short historical dataset does Middle Ground Shelf EWMA August 2009 not adequately represent the full range of within and between year variation that may occur at this site.

The result is within the historical data range indicating that results of similar and Dromana Shewhart September 2009 greater magnitude have occurred at this site previously. The exceedence was localised with values returning below control limits by October 2009.

This is the first occasion since the commencement of the Baywide Monitoring Program that the control limits have been exceeded. Control limits are based on a Total Nitrogen (TN) Yarra River at Newport EWMA September - October 2009 limited historical dataset (collected during sustained period of drought) that does not adequately represent the full range of within and between year variation that may

PARAMETER SITES EXCEEDENCE TYPE DATES ASSESSMENT OUTCOME occur at this site. Evidence suggests that these results are likely to be due to seasonal trends. On-going monthly monitoring results at this site will continue to be Shewhart October 2009 assessed to determine if there is a longer term shift in NOx and TN.

This exceedence was a result of elevated values reported in the previous months EWMA November 2009 as the November 2009 raw value was below the control limit.

This exceedence is most likely a result of increased catchment inputs into the Yarra EWMA December 2009 River following rainfall. This pattern of exceedence is also reflected in the NOx Shewhart exceedences reported at this site.

The result was a marginal exceedence outside of the limited historical data range that was most likely a result of instrumental and/or laboratory measurement of Total Chromium Yarra River at Newport Shewhart September 2009 uncertainty. The dissolved (bio-available) fraction was below the ANZECC objective (<1ug/L) and is not considered biologically significant.

The dissolved metal fraction is readily available for uptake by organisms. The dissolved fraction (2 µg/L) was greater than the total fraction (<1 µg/L) and it is likely Dissolved Copper Dromana SEPP (ANZECC) August 2009 that the elevated dissolved fraction of copper at this site is indicative of instrumental and/or lab measurement uncertainty.

The result was localised and marginally outside of the historical data range. The Total Zinc Corio Bay SEPP September 2009 dissolved (bio-available) concentration was below the SEPP objective (<5 µg/L). It is not considered biologically significant and was identified as a transient elevation.

The dissolved metal fraction is readily available for uptake by organisms. This is the Dissolved Zinc Yarra River at Newport SEPP (ANZECC) August 2009 second consecutive dissolved zinc exceedence however the total zinc concentration was below the Shewhart limit and is within the historical range.

The total zinc value was outside of the historical range (based on a limited dataset) Shewhart Total and dissolved zinc Yarra River at Newport December 2009 for this site. The exceedence of both total and dissolved zinc was most likely a SEPP (ANZECC) result of increased catchment inputs into the Yarra River during December 2009.

Total and dissolved Shewhart This result is considered marginal (at the LOR) and transient as mercury was not Yarra River at Newport November 2009 mercury SEPP recorded in December 2009.

Dissolved mercury Central Bay SEPP (ANZECC) November 2009 These results are considered marginal (at the LOR) and transient as mercury was not recorded in December 2009. Middle Ground Shelf PoM DMG Patterson River Sorrento Bank

PARAMETER SITES EXCEEDENCE TYPE DATES ASSESSMENT OUTCOME Popes Eye

APPENDIX 6. - SUMMARY STATISTICS (JANUARY – DECEMBER 2009)

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 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 2.7 <0.5 16 <0.2 <1 1.2 <0.2 <0.1 Minimum 1.4 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 3.1 <0.5 20 <0.2 1 1.2 0.3 0.1 N 12 12 12 12 12 12 12 12

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 95 32.6 17.1 7.8 12.8 Median 93 34.6 17.3 5.8 <20 9.6 <25 90th percentile 100 36.3 22.1 15.3 <50 24.9 <60 Minimum 88 >60 25.0 11.3 2.2 5.6 Maximum 116 36.8 22.9 24.3 29.1 N 12 12 12 12 12

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

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

SEPP objective µµµg/L <3 <5 <10 <5.5 <1.3 <70 <4.4 <0.4 <0.006 Mean 2.3 Median 2.2 0.6 5 <0.2 <1 0.8 <0.2 <0.1 <0.002 90th percentile 2.8 1.6 14 <0.2 <1 1.2 <0.2 <0.1 <0.002 Minimum 1.5 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 <0.002 Maximum 3.2 1.7 20 <0.2 1 1.2 0.3 0.1 <0.003 N 12 12 12 12 12 12 12 12 12

Dissolved Dissolved Secchi Secchi Oxygen Oxygen Salinity Temperature Depth Depth Chlorophyll-a Chlorophyll-a SEPP SEPP SEPP objective objective objective %sat %sat mg/L deg C metres metres µµµg/L µµµg/L Mean 95 32.6 17.1 0.9 2.55 Median 93 34.6 17.3 1.0 1.91 2.5 90th percentile 100 36.3 22.1 1.3 4.91 4.0 Minimum 88 >90 25.0 11.3 0.2 >2 0.70 Maximum 116 36.8 22.9 1.7 8.16 N 12 12 12 12 12

Table A6.3 Hobsons Bay summary statistics

Total Total Dissolved Dissolved Dissolved Dissolved Dissolved Tributyl Arsenic Chromium Total Zinc Cadmium Copper Nickel Lead Mercury Tin SEPP objective µµµg/L <3 <5 <10 <5.5 <1.3 <70 <4.4 <0.4 <0.006 Mean 2.4 Median 2.3 <0.5 <5 <0.2 <1 0.6 <0.2 <0.1 <0.002 90th percentile 2.9 0.9 <5 <0.2 <1 0.7 0.3 <0.1 <0.002 Minimum 1.7 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 <0.002 Maximum 3.0 1.4 7 0.2 <1 0.7 0.3 0.1 <0.002 N 12 12 12 12 12 12 12 12 12

percentile 105 37.5 20.6 3.8 2.30 4.0 Minimum 92 >90 34.9 11.1 0.3 >2 0.57 Maximum 107 37.6 21.6 4.3 2.99 N 12 12 12 12 12

Table A6.4 Corio Bay summary statistics

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 Median 2.5 <0.5 <0.5 <0.2 <1 0.8 <0.2 <0.1 90th percentile 3.4 <0.5 9 0.2 <1 1.0 <0.2 <0.1 Minimum 1.8 <0.5 <0.5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 3.8 0.7 15 0.2 1 1.0 0.3 0.1 N 12 12 12 12 12 12 12 12

percentile 104 38.7 21.3 2.17 2.5 Minimum 91 >90 37.4 10.1 1.9 >3 0.63 Maximum 110 38.7 21.7 >6.4 2.54 N 12 12 12 12 12

Table A6.5 Long Reef summary statistics

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 0.7 <0.2 <0.1 90th percentile 2.9 0.6 <5 <0.2 <1 1.0 <0.2 <0.1 Minimum 1.8 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.9 1.0 <5 0.2 <1 2.1 <0.2 0.1 N 12 12 12 12 12 12 12 12

Dissolved Dissolved Secchi Secchi Oxygen Oxygen Salinity Temperature Depth Depth Chlorophyll-a Chlorophyll-a SEPP SEPP SEPP objective objective objective %sat %sat mg/L deg C metres metres µµµg/L µµµg/L Mean 98 37.3 16.2 1.11 Median 97 37.3 15.7 0.96 2.5 90th percentile 106 37.9 21.2 1.56 4.0 Minimum 91 >90 36.4 9.8 1.2 >3 0.60 Maximum 107 38.2 21.9 >5.9 2.57 N 12 12 12 12 12

Table A6.6 Central Bay summary statistics

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 2.4 Median 2.4 <0.5 <5 <0.2 <1 0.5 <0.2 <0.1 90th percentile 2.8 <0.5 7 <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 0.6 7 0.2 <1 0.7 <0.2 0.1 N 12 12 12 12 12 12 12 12

Dissolved Dissolved Secchi Secchi Oxygen Oxygen Salinity Temperature Depth Depth Chlorophyll-a Chlorophyll-a SEPP SEPP SEPP objective objective objective %sat %sat mg/L deg C metres metres µµµg/L µµµg/L Mean 97 37.1 16.3 8.5 0.61 Median 96 37.1 16.7 7.8 0.60 1.0 90th >90 percentile 100 37.6 19.9 11.6 0.96 2.0 Minimum 93 >90 36.5 10.8 4.2 >4 0.25 Maximum 102 37.6 22.0 13.0 1.05 N 12 12 12 12 12

Table A6.7 POM DMG summary statistics

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 2.4 <0.5 <5 <0.2 <1 0.5 <0.2 <0.1 90th percentile 2.9 <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 2.9 0.5 7 0.2 <1 0.8 0.3 0.1 N 12 12 12 12 12 12 12 12

Dissolved Dissolved Secchi Secchi Oxygen Oxygen Salinity Temperature Depth Depth Chlorophyll-a Chlorophyll-a SEPP SEPP SEPP objective objective objective %sat %sat mg/L deg C metres metres µµµg/L µµµg/L Mean 97 37.1 16.3 7.0 0.68 Median 96 37.1 16.7 7.7 0.72 1.0 90th >90 percentile 99 37.6 20.3 12.1 1.01 2.0 Minimum 93 >90 36.5 10.6 2.4 >4 0.26 Maximum 107 37.7 22.1 12.6 1.11 N 12 12 12 12 12

Table A6.8 Patterson River summary statistics

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 2.4 Median 2.4 <0.5 <5 <0.2 <1 0.6 <0.2 <0.1 90th percentile 2.9 <0.5 8 <0.2 <1 0.7 0.2 <0.1 Minimum 1.8 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 Maximum 2.9 0.9 15 0.2 <1 0.7 0.3 0.1 N 12 12 12 12 12 12 12 12

percentile 99 37.4 19.5 1.06 2.5 Minimum 92 >90 33.0 10.7 2.9 >3 0.35 Maximum 104 37.4 21.8 >8.2 2.88 N 12 12 12 12 12

Table A6.9 Dromana summary statistics

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 2.2 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 90th percentile 2.8 0.7 <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 2.9 2.2 <5 <0.2 2 0.6 0.6 0.1 N 12 12 12 12 12 12 12 12

Dissolved Dissolved Secchi Secchi Oxygen Oxygen Salinity Temperature Depth Depth Chlorophyll-a Chlorophyll-a SEPP SEPP SEPP objective objective objective %sat %sat mg/L deg C metres metres µµµg/L µµµg/L Mean 97 36.8 16.2 0.59 Median 97 36.8 16.6 0.48 1.5 90th percentile 100 37.3 19.8 0.93 2.5 Minimum 94 >90 36.4 11.1 2.9 >3 0.28 Maximum 101 37.4 21.4 >7.1 1.52 N 12 12 12 12 12

Table A6.10 Middle Ground Shelf summary statistics

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 2.8 <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 3.0 0.7 <5 0.2 <1 0.7 <0.2 0.1 N 12 12 12 12 12 12 12 12

Dissolved Dissolved Secchi Secchi Oxygen Oxygen Salinity Temperature Depth Depth Chlorophyll-a Chlorophyll-a SEPP SEPP SEPP objective objective objective %sat %sat mg/L deg C metres metres µµµg/L µµµg/L Mean 97 36.9 16.3 7.2 0.67 Median 97 36.9 17.0 6.9 0.58 1.0 90th >90 percentile 100 37.3 19.8 10.3 1.07 2.0 Minimum 94 >90 36.3 11.1 2.5 >4 0.26 Maximum 100 37.3 21.2 10.5 1.10 N 12 12 12 12 12

Table A6.11 Sorrento Bank summary statistics

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 0.6 <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 0.8 <5 0.2 <1 1.3 0.4 0.1 N 12 12 12 12 12 12 12 12

Dissolved Dissolved Secchi Secchi Oxygen Oxygen Salinity Temperature Depth Depth Chlorophyll-a Chlorophyll-a SEPP SEPP SEPP objective objective objective %sat %sat mg/L deg C metres metres µµµg/L µµµg/L Mean 98 36.2 16.2 0.67 Median 97 36.2 16.6 0.66 1.0 90th >90 percentile 101 36.5 19.8 0.83 2.0 Minimum 94 >90 35.7 11.6 >4 0.34 Maximum 104 36.6 20.2 >4.0 1.41 N 12 12 12 12 12

Table A6.12 Popes Eye summary statistics

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 1.9 Median 1.9 <0.5 <5 <0.2 <1 <0.5 <0.2 <0.1 90th percentile 2.2 0.7 <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 2.7 1.0 <5 0.2 <1 0.6 0.2 0.1 N 12 12 12 12 12 12 12 12

Dissolved Dissolved Secchi Secchi Oxygen Oxygen Salinity Temperature Depth Depth Chlorophyll-a Chlorophyll-a SEPP SEPP SEPP objective objective objective %sat %sat mg/L deg C metres metres µµµg/L µµµg/L Mean 97 36.0 16.3 0.58 Median 97 35.7 16.8 0.49 1.0 90th >90 percentile 101 36.4 18.9 0.88 2.0 Minimum 93 >90 35.6 12.7 7.0 >4 0.24 Maximum 102 37.3 19.6 >13.3 1.04 N 12 12 12 9 12

APPENDIX 7. - ERRATA

October 2009

Exception Report ER091001

An error was made during transcription of data when preparing Progress Report No 1. Metals values for Patterson River were reported as Dromana values and vice versa (Table A7.1). This error subsequently also resulted in incorrect calculation and reporting of arsenic EWMAs for these two sites (Table A7.2). This error has also resulted in incorrect reporting for these analytes and sites has also been repeated in Milestone Reports No 1-2 and Progress Report No 3, either as values reported in tables or as values shown in control charts.

Table A7.1 Summary of changes to metals values reported in Progress Report No.1

Sampling Site Date Parameter Depth Concentration m ug/L

Published Revised value value Arsenic 0.5 2.2 2.8 Copper 0.5 <1 5 Patterson River 1/11/2007 Nickel 0.5 <0.5 1.2 Lead 0.5 <0.2 0.5 Zinc 0.5 <5 17 Arsenic 0.5 2.8 2.2 Copper 0.5 5 <1 Dromana 1/11/2007 Nickel 0.5 1.2 <0.5 Lead 0.5 0.5 <0.2 Zinc 0.5 17 <5

Above Shewhart Limit Above SEPP/ANZECC Objective

BAYWIDE WATER QUALITY MONITORING PROGRAM — MILESTONE REPORT NO. 5

Table A7.2 Summary of changes to arsenic EWMA values reported in Milestone Reports No.1 and 2 and Progress Report No.3 Published Revised Sampling site Date Parameter EWMA EWMA 01/11/07 2.26 2.4 23/01/08 2.36 2.5 Patterson River 21/02/08 2.57 2.7 19/03/08 2.7 2.8 Arsenic 01/11/07 2.34 2.2 29/11/07 2.39 2.3 Dromana 22/01/08 2.45 2.4 21/02/08 2.58 2.5

Above EWMA Limit

100