Title page 1

Contents 3

COMMONLY USED ABBREVIATIONS AND ACRONYMS 7

ACKNOWLEDGEMENTS 8

EXECUTIVE SUMMARY 9

Wet Tropics region coral community condition 10

Burdekin region coral community condition 11

Mackay-Whitsunday region coral community condition 11

Fitzroy region coral community condition 11

1. INTRODUCTION 13

1.1. Conceptual basis for coral monitoring program 13

1.2. Purpose of this report 14

2. METHODS 15

2.1. Climate and environmental pressures 15

2.1.1. River discharge 15

2.1.2. River nutrient and sediment loads 15

2.1.3. Sea temperature 16

2.1.4. Temperature stress 16

2.1.5. Cyclone tracks 19

2.1.6. Water quality 19

2.2. Coral monitoring 21

2.2.1. Sampling design 21

2.2.2. Site selection 21

2.2.3. Depth selection 23

2.2.4. Site marking 23

2.2.5. Sampling timing and frequency 23

2.3. Coral community sampling methods 25

2.3.1. Photo point intercept transects 25

2.3.2. Juvenile coral transects 25

2.3.3. SCUBA search transects 26

2.4. Calculating Reef Water Quality Report Card coral scores 27

2.4.1. Coral cover indicator metric 27

2.4.2. Macroalgae indicator metric 28

2.4.3. Juvenile coral indicator metric 29

2.4.4. Cover change indicator metric 30

2.4.5. Composition indicator metric 32

2.4.6. Aggregating indicator scores to Reef and regional scale assessments 33

2.5. Data analysis and presentation 35

2.5.1. Variation in Coral Index and indicator scores to gradients in water quality 35

2.5.2. Relationship between Coral Index scores and environmental conditions 36

2.5.3. Temporal trends in Coral Index and indicators 36

2.5.4. Analysis of change in Coral Index and indicator scores 36

2.5.5. Response to pressures 36

3. PRESSURES INFLUENCING CORAL REEFS 38

3.1. Cyclones 38

3.2. Sea temperature 38

3.3. Crown-of-thorns starfish 41

3.4. River discharge 43

3.5. Water quality 44

4. CORAL COMMUNITY CONDITION AND TRENDS 45

4.1. Reef-wide coral community condition and trend 45

4.2. Reef-wide relative impact of disturbances 46

4.3. Wet Tropics region 48

4.3.1. Regional trend 48

4.3.2. Barron-Daintree sub-region 49

4.3.3. Johnstone Russell-Mulgrave sub-region 53

4.3.4. Herbert-Tully sub-region 57

4.4. Burdekin region 61

4.5. Mackay-Whitsunday region 65

4.6. Fitzroy region 69

4.7. Response of coral communities to environmental conditions 74

4.7.1. Location along water quality gradients 74

4.7.2. Influence of discharge, catchment loads and water quality on reef recovery 78

5. DISCUSSION 79

5.1. Pressures 79

5.1.1. Acute disturbances 79

5.1.2. Chronic conditions - water quality 81

5.2. Ecosystem state 83

5.2.1. Reef-wide coral community condition based on the Coral Index 83

5.2.2. Wet Tropics Region 84

5.2.3. Burdekin Region 86

5.2.4. Mackay-Whitsunday Region 87

5.2.5. Fitzroy Region 88

5.3. Indicators 89

5.3.1. Coral cover 89

5.3.2. Rate of change in coral cover 90

5.3.3. Community composition 92

5.3.4. Macroalgae 93

5.3.5. Juvenile coral density 95

5.4. Management response 96

6. CONCLUSIONS 97

7. REFERENCES 99

APPENDIX 1: ADDITIONAL INFORMATION 114

APPENDIX 2: PUBLICATIONS AND PRESENTATIONS 2023-2024 162

Publications 162

Presentations 162

Tables 5

Table 1. Summary of climate and environmental data considered in this report 18

Table 2. Water types estimated from Sentinel imagery 20

Table 3. Coral monitoring samples 24

Table 4. Survey methods used by the MMP and LTMP to describe coral communities 25

Table 5. Categories used to record proportion of corals bleached or physically damaged 26

Table 6. Threshold values for the assessment of coral reef condition and resilience indicators 34

Table 7. Format for presentation of community condition 35

Table 8. Information considered for disturbance categorisation 37

Table 9. Numbers of crown-of-thorns starfish observed along scuba search transects 41

Table 10. Number of crown-of-thorns removed 42

Table 11. Size class distribution of crown-of-thorns starfish on inshore reefs in the Wet Tropics 42

Table 12. Barren-Daintree sub-region Coral Index and indicator score changes 50

Table 13. Johnstone Russell-Mulgrave sub-region Coral Index and indicator score changes 53

Table 14. Herbert-Tully sub-region Coral Index and indicator score changes 57

Table 15. Burdekin region Coral Index and indicator score changes 61

Table 16. Mackay-Whitsunday region Coral Index and indicator score changes 65

Table 17. Fitzroy region Coral Index and indicator score changes 69

Table 18. Indicator score and value relationships with satellite derived and water quality 74

Table 19. Relationships between coral reef communities and measured water quality 75

Figures 5

Figure 1. Trends in the Coral Index and contributing indicator scores for the inshore Reef 9

Figure 2. Coral sampling locations 2024 22

Figure 3. Scoring diagram for the Coral cover indicator metric 28

Figure 4. Scoring diagram for the Macroalgae indicator metric 29

Figure 5. Scoring diagram for the Juvenile coral indicator metric 30

Figure 6. Scoring diagram for Cover change indicator metric 32

Figure 7. Scoring diagram for the Composition indicator metric 33

Figure 8. Cyclone tracks for systems crossing the inshore Reef since 2006 39

Figure 9. Annual DHW estimates for the Reef 40

Figure 10. Annual total river discharge to the Reef 43

Figure 11. The Reef level trend in Coral Index and indicator scores 45

Figure 12. Hard coral cover loss by disturbance type across the inshore Reef 46

Figure 13. Proportion of hard coral cover bleached at the time of survey in 2024 47

Figure 14. Wet Tropics region Coral Index and indicator trends 48

Figure 15. Barron-Daintree sub-region Coral Index and indicator trends 49

Figure 16. Barron-Daintree sub-region environmental pressures 51

Figure 17. Barron-Daintree sub-region indicator trends 52

Figure 18. Johnstone Russell-Mulgrave sub-region Coral Index and indicator trends 53

Figure 19. Johnstone Russell-Mulgrave sub-region environmental pressures 55

Figure 20. Johnstone Russell-Mulgrave sub-region indicator trends 56

Figure 21. Herbert-Tully sub-region Coral Index and indicator trends 57

Figure 22. Herbert-Tully sub-region environmental pressures 59

Figure 23. Herbert-Tully sub-region indicator trends 60

Figure 24. Burdekin region Coral Index and indicator trends 61

Figure 25. Burdekin region environmental pressures 63

Figure 26. Burdekin region indicator trends 64

Figure 27. Mackay-Whitsunday region Coral Index and indicator trends 65

Figure 28. Mackay-Whitsunday region environmental pressures 67

Figure 29. Mackay-Whitsunday region indicator trends 68

Figure 30. Fitzroy region Coral Index and indicator trends 69

Figure 31. Distribution of bleaching among hard coral families in the Fitzroy region in May 2024 70

Figure 32. Fitzroy region environmental pressures 72

Figure 33. Fitzroy region indicator trends 73

Figure 34. Cover change score relationships.Chl a and light attenuation coefficient (Kd 490) 74

Figure 35. Hard coral community composition relationships to Chl a and light attenuation (Kd 490) 75

Figure 36. Coral cover indicator score relationships to water quality 75

Figure 37. Macroalgae cover relationships to water quality at 2 m depth 76

Figure 38. Macroalgae proportion to water quality relationships 76

Figure 39. Relationship between coral community composition values and water quality 77

Figure 40. Relationship between the Coral Index and freshwater discharge from local catchments 78

Appendix Tables 7

Table A1. Source of river discharge data used for daily discharge estimates 114

Table A2. Temperature loggers used 114

Table A3. Thresholds for the proportion of macroalgae in the algae communities 115

Table A4. Eigenvalues for hard coral genera along constrained water quality axis 116

Table A5. Annual freshwater discharge for the major Reef Catchments 117

Table A6. Disturbance records for each survey reef 118

Table A7. Reef-level Coral Index and indicator scores 2024 123

Table A8. Environmental covariates for coral locations 125

Table A9. Percent cover of hard coral genera 2024 146

Table A10. Percent cover of soft coral families 2024 149

Table A11. Percent cover of macroalgae groups 2024 152

Appendix Figures 7

Figure A1. Barron-Daintree sub-region benthic community composition 126

Figure A2. Johnstone Russell-Mulgrave sub-region benthic community composition 127

Figure A3. Herbert-Tully sub-region benthic community composition 130

Figure A4. Burdekin region benthic community composition 132

Figure A5. Mackay-Whitsunday region benthic community composition 136

Figure A6. Fitzroy region benthic community composition 140

Figure A7. Proportion of hard coral bleached in each sub-region at the time of surveys 142

Figure A8. Coral disease by year in each region 143

Figure A9. Crown-of-thorn-starfish mean density (individuals/ha) by year in each region 144

Figure A10. Mean density of Drupella by year in each (sub-)region 145

Figure A11. Temporal trends in water quality: Barron-Daintree sub-region 156

Figure A12. Temporal trends in water quality: Johnstone Russell-Mulgrave sub-region 157

Figure A13. Temporal trends in water quality: Herbert-Tully sub-region 158

Figure A14. Temporal trends in water quality: Burdekin region 159

Figure A15. Temporal trends in water quality: Mackay-Whitsunday region 160

Figure A16. Temporal trends in water quality: Fitzroy region 161