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Title page

Contents

List of Acronyms 10

1. Introduction 12

1.1. Threats to the Great Barrier Reef from anthropogenic-sourced poor water quality 12

1.2. Halting and reversing the decline in water quality 13

1.3. The Marine Monitoring Program 13

1.3.1. Inshore Marine Water Quality Monitoring 15

1.3.2. Remote sensing of water quality 16

1.3.3. Pesticide monitoring 16

1.3.4. Inshore seagrass monitoring 17

1.3.5. Inshore coral monitoring 18

1.3.6. Synthesis of data and integration 18

1.4. Marine Monitoring Program Quality Assurance and Quality Control Methods and Procedures 19

2. Inshore marine water quality monitoring 21

2.1. Introduction 21

2.2. Methods 23

2.2.1. Sampling locations and frequency 23

2.2.2. Sample collection, preparation and analysis (JCU) 30

2.2.3. Sample collection, preparation and analysis - AIMS 34

2.2.4. Autonomous environmental water quality loggers 36

2.2.5. Sample collection, preparation and analysis - wet season - event response (JCU) 37

2.3. Data management 38

2.4. Summary of Quality Control measures 39

2.5. Comparison of results obtained by AIMS and JCU 39

3. Remote sensing of the Great Barrier Reef wet season water quality and river plumes 42

3.1. Introduction 42

3.2. Methods 43

3.2.1. MODIS satellite data 43

3.2.2. MODIS true colour monitoring products 44

3.3. Automated production and storage of the MODIS wet season water type maps 46

3.3.1. From L0 to true colour MODIS data 46

3.3.2. Maps of wet season water types and flood plumes 47

3.3.3. Derived monitoring products 47

3.4. Marine water quality metric 48

4. Pesticide monitoring 50

4.1. Introduction 50

4.2. Methods 51

4.2.1. Sampling design - Passive sampling for routine monitoring 51

4.2.2. Sampling design - Flood Plume Grab sampling 54

4.2.3. Target Pesticides in the different passive samplers 54

4.2.4. Chemical Analysis 57

4.2.5. Passive Sampling Techniques 58

4.2.6. QA/QC procedures in the pesticide monitoring program 68

4.3. Data Management & Security 69

4.4. Summary 70

5. Inshore coral reef monitoring 72

5.1. Introduction 72

5.2. Methods 73

5.2.1. Sampling design 73

5.2.2. Site selection 74

5.2.3. Depth selection 75

5.2.4. Field survey methods 75

5.2.5. Observer training 80

5.2.6. Temperature monitoring 81

5.3. Data management 82

5.4. Summary of Quality Control measures 83

6. Inshore seagrass monitoring 84

6.1. Introduction 84

6.2. Methods 84

6.2.1. Sampling design 84

6.2.2. Field survey methods - Inshore seagrass meadow abundance, community structure and reproductive health 85

6.2.3. Observer training 91

6.2.4. Laboratory analysis - Inshore seagrass meadow abundance, community structure and reproductive health 91

6.2.5. Sampling design - Inshore seagrass meadow boundary mapping 94

6.2.6. Sampling design - Within seagrass canopy temperature loggers 95

6.2.7. Sampling design and logistics - Seagrass meadow canopy light loggers 96

6.2.8. Calibration procedures - Seagrass meadow canopy light loggers 98

6.3. Data management 99

6.3.1. Inshore seagrass meadow abundance, community structure and reproductive health 99

6.3.2. Inshore seagrass meadow boundary mapping 99

6.3.3. Within seagrass canopy temperature loggers 100

6.3.4. Seagrass meadow canopy light loggers 100

6.4. Summary of Quality Control measures 100

6.4.1. Inshore seagrass meadow abundance, community structure and reproductive health 100

6.4.2. Inshore seagrass meadow boundary mapping 101

6.4.3. Within seagrass canopy temperature loggers 101

6.4.4. Seagrass meadow canopy light loggers 101

7. References 102

Appendix A. Detailed AIMS Manuals and Standard Operational Procedures 110

Section A1: Operating instructions for the AIMS Sea-Bird CTD 113

Section A2: Salinity measurements using Guildline Portasal Salinometer Model 8410A 118

Section A3: Automated analysis of dissolved nutrients in seawater 128

Section A4: Ship board ammonium analysis using the OPA method 137

Section A5: Analysis of dissolved organic carbon 155

Section A6: Analysis of Chromophoric Dissolved Ocean Matter (CDOM) in marine waters 161

Section A7: Analysis of particulate phosphorus in marine waters 167

Section A8: Analysis of particulate organic carbon and particulate nitrogen in marine waters 177

Section A9: Analysis of chlorophyll a in marine waters 188

Section A10: Determination of total suspended solids in marine waters 204

Section A11: AIMS In-house procedures for WET Labs FLNTUSB ECO logger 214

Section A12: AIMS Data Management Procedures for the Marine Monitoring Program 275

Appendix B. James Cook University TropWater Appendices 285

Appendix B1. TropWater Water Sampling Procedures 286

Appendix B2. TropWater Water Sampling Field Sheet - Example 289

Appendix B3. Metadata for flood plume data entered into TropWater flood database 291

Appendix B4. TropWater Water Sampling Input Sheet 308

Appendix B5. TropWater Auto-analysis methods: Nitrogen - Ammonia 309

Appendix B6. TropWater Auto-analysis methods: Phosphorus (Filterable Reactive) 326

Appendix B7. TropWater Auto-analysis methods: Nitrate and Nitrite 343

Appendix B8. TropWater Auto-analysis methods: Nitrogen - Total Alkaline Persulfate 361

Appendix B9. TropWater Auto-analysis methods: Phosphorus - Total Alkaline Persulfate 380

Appendix B10. TropWater Auto-analysis methods: Chlorophyll 398

Appendix B11. TropWater Auto-analysis methods: Total Suspended Solids 406

Tables

Table 1.1. MMP current monitoring themes, sub-programs and monitoring providers. Note that a project may contribute to more than one sub-program 14

Table 2.1. Great Barrier Reef inshore water quality monitoring locations by NRM regions. Monitoring is a collaborative effort between JCU and AIMS. Indicates sites where pesticide passive samplers are deployed 24

Table 2.2. Summary of the sampling protocols with identification of post-sampling procedures needed, laboratory containers required, and storage technique 33

Table 3.1. MODIS monitoring products. "Annual" refers to the wet season only (c.a., December to April, inclusive) 44

Table 3.2. Keywords and justification used in SeaDAS 7.4 to process MODIS true colour images of the GBR 47

Table 4.1. Types of passive sampling which was conducted at each of the routine monitoring sites in 2016-2017 during either the dry (May-October) or wet (November-April) periods 53

Table 4.2. Pesticides specified under the MMP for analysis in different passive sampler extracts and water samples together with the approximate instrument Limits of Detection (LOD) and Limits of Reporting... 55

Table 4.3. Interim risk classes used for 2014-15 and 2015-16 reporting years for the ms-PAF method 64

Table 5.1. Sites selected for inshore reef monitoring 78

Table 5.2. Distribution of sampling effort 79

Table 5.3. Observer training methods and quality measures 81

Table 6.1. MMP inshore seagrass long-term monitoring sites 87

Table 6.2. Additional inshore seagrass long-term monitoring sites from the Seagrass-Watch and QPWS drop-camera programs integrated into MMP 89

Table 6.3. Monitoring sites selected for light logger data collection 97

Figures

Figure 2-1. MMP water quality sampling sites in the Cape York region shown with water body boundaries 27

Figure 2-2. MMP water quality sampling sites in the Wet Tropics region including the Barron Daintree, Russell-Mulgrave and Tully focus areas, shown with water body boundaries 28

Figure 2-3. Sampling MMP sampling sites in the Burdekin focus area, shown with the water body boundaries 29

Figure 2-4. Sampling locations under the MMP inshore marine water quality task for the Mackay- Whitsunday regions 29

Figure 2-5. Relationships between (a) salinity, (b) Total suspended solids (TSS), (c) Chlorophyll a (Chl a), (d) silicate, (e) nitrate and (f) phosphate measured by AIMS and JCU respectively. Solid lines represent a linear regression 40

Figure 3-1. Summary description of the wet season water quality products from remote sensing information in the MMP (modified from Devlin et al 2015) 43

Figure 4-1. Purple dots indicate the locations of the eleven inshore Reef routine monitoring sites where time-integrated sampling of pesticides occurred from the 2014 monitoring year onwards 52

Figure 4-2. An Empore disk (ED) being loaded into the Teflon Chemcatcher housing (LHS) and an assembled housing ready for deployment (RHS) 59

Figure 4-3. Passive flow monitors (PFMs) prior to deployment (LHS) and post-deployment (RHS) 60

Figure 4-4. The relationship between flow and the sampling rates of specific herbicides indicating a shift from aqueous boundary layer control to diffusion limiting membrane control under higher flow conditions 60

Figure 4-5. Overview of approach to determine a multi-substance species sensitivity distribution (SSD) for a mixture of herbicides with the same mode of action (concentration additive model).... 63

Figure 4-6. PDMS passive samplers loaded onto stainless steel sampler supports which sits within the deployment cage and is sealed in place with wing nuts 66

Figure 4-7. PDMS and SPMD sampling rates (Rs) as a function of water velocity rPFM 67

Figure 4-8. A schematic for the deployment of passive samplers (Empore disc in Chemcatcher housings, and /PDMS cages) together with the passive flow monitors (PFMS) for in-situ calibration of flow effects, in the field 68

Figure 5-1. Sampling design for coral reef benthic community monitoring. Terms within brackets are nested within the term appearing 74

Figure 5-2. Coral community sampling locations as at 2015, including sites surveyed under the AIMS Long Term Monitoring Program 77

Figure 6-1. Inshore seagrass monitoring sites for the Marine Monitoring Program 86

Figure 6-2. Form and size of reproductive structure of the seagrasses collected: Halophila ovalis, Halodule uninervis and Zostera muelleri subsp. capricorni 92

Appendix Figures

Section A4: Ship board ammonium analysis using the OPA method 146

Figure 1. Rear view of Trilogy 146

Figure 2. showing Optical Kit installed in preparation for getting to the Home Screen 147

Figure 3. Module Selection Screen 147

Figure 4. Trilogy Home Screen Display for Fluorescence Module Configuration 148

Figure 5/Figure 6. Trilogy Home Screen for Fluorescence Module Configuration 149

Section A7: Analysis of particulate phosphorus in marine waters 175

Fig. 1. Hand held hobby engraver with custom built shaft 175

Fig. 2. Detail of modified shaft 175

Section A10: Determination of total suspended solids in marine waters 211

Fig. 1. 25 mm and 47 mm filter bases 211

Fig. 2. Pre-weighed filter in labelled bottle 211

Fig. 3. Placing suspended solids 211

Fig. 4. 47mm filter 211

Fig. 5. Washing down funnel walls 213

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