METHODS FOR THE MACKAY-WHITSUNDAY-ISAAC 2018 REPORT CARD ENVIRONMENTAL INDICATORS Authorship statement The Mackay-Whitsunday-Isaac Healthy Rivers to Reef Healthy Partnership (Partnership) Methods for Environmental Indicators for the Mackay-Whitsunday-Isaac 2018 Report Card technical report was compiled by the Partnership’s Technical Officers, Alysha Lee and Jessica Gillespie. Substantial input was received from the Regional Report Cards Technical Working Group (TWG) members. Some content was also drawn from technical reports from earlier Mackay-Whitsunday- Isaac report cards. Regional Report Cards Technical Working Group members Diane Tarte (TWG Chair July 2018 onwards) Adam Fletcher Paulina Kaniewska Nicola Stokes Richard Hunt Reinier Mann Tegan Whitehead Angus Thompson Emma Maxwell Nathan Waltham Alysha Lee Alex Carter Jessica Gillespie Michael Rasheed Carl Mitchell Glynis Orr Nyssa Henry Luke Galea Michael Holmes Eddie Jebreen David Moffatt Ken Rhode Andrew Moss Travis Sydes Lynne Powell Lyndon Llewellyn Judith Wake Nadine Marshall Donna Audas Paul Groves Chris Dench Stephen Lewis Michael Nash Chris Manning Melinda Louden Adam Folkers Acknowledgements The authors also thank Phillip Trendell, Bernie Cockayne, Bronwyn Houlden, Carol Honchin, Len McKenzie, Jamie Corfield and Matt Curnock for their technical input into various aspects of document development and/or their review of the document. Members of the Reef Independent Science Panel are also gratefully acknowledged for their advice and review of this document. Suggested citation Mackay-Whitsunday-Isaac Healthy Rivers to Reef Partnership (2019). Methods for the Mackay- Whitsunday-Isaac 2018 Report Card: Environmental Indicators, Technical Report. Mackay- Whitsunday-Isaac Healthy Rivers to Reef Partnership, Mackay. This technical report was finalised and released online in November 2019. Table of Contents Terms and Acronyms .............................................................................................................................. 6 1. Introduction .................................................................................................................................... 9 1.1. Purpose of this document ............................................................................................................... 9 1.2. Background ..................................................................................................................................... 9 1.3. Terminology .................................................................................................................................. 10 2. Data collection methods ............................................................................................................... 11 2.1. Freshwater basins ......................................................................................................................... 12 2.1.1. Water quality index ............................................................................................................... 12 2.1.1.1. Sediment, nutrients and pesticides ...................................................................................... 13 2.1.2. Habitat and hydrology index ................................................................................................. 15 2.1.2.1. In-stream habitat modification ............................................................................................. 15 2.1.2.2. Flow ....................................................................................................................................... 18 2.1.2.3. Riparian extent ...................................................................................................................... 21 2.1.2.4. Wetland extent ..................................................................................................................... 21 2.1.3 Fish index .............................................................................................................................. 22 2.2. Estuaries ........................................................................................................................................ 24 2.2.1. Water quality index ............................................................................................................... 24 2.2.1.1. Nutrients, phys-chem and pesticides .................................................................................... 24 2.2.2. Habitat and hydrology index ................................................................................................. 26 2.2.2.1. Riparian extent ...................................................................................................................... 26 2.2.2.2. Mangrove/saltmarsh extent ................................................................................................. 26 2.2.2.3. Flow ....................................................................................................................................... 27 2.2.2.4. Fish barriers ........................................................................................................................... 27 2.2.3. Fish index .............................................................................................................................. 29 2.3. Inshore and Offshore marine environments ................................................................................ 30 2.3.1. Water quality index ............................................................................................................... 30 2.3.1.1. Inshore nutrients, chlorophyll-a, water clarity and pesticides ............................................. 30 2.3.1.2. Offshore sediment and chlorophyll-a ................................................................................... 34 2.3.2. Coral index ............................................................................................................................ 34 2.3.2.1. Sampling programs and survey methods ............................................................................. 34 2.3.3. Seagrass index ....................................................................................................................... 37 2.3.3.1. Marine Monitoring Program ................................................................................................. 38 2.3.3.2. Queensland Ports Seagrass Monitoring Program ................................................................. 39 2.3.4. Fish index .............................................................................................................................. 39 3 Development of condition assessments scoring methods ........................................................... 41 3.1 Freshwater basins and estuaries................................................................................................... 42 3.1.3 Water quality index ............................................................................................................... 42 3.1.3.1. Nutrients, sediments and phys-chem ................................................................................... 42 3.1.3.2. Pesticides .............................................................................................................................. 46 3.1.4 Habitat and hydrology .......................................................................................................... 47 3.1.4.1. Habitat Modification/instream habitat modification (freshwater basins) ........................... 47 3.1.4.2. Fish barriers (estuaries)......................................................................................................... 49 3.1.4.3. Flow (Freshwater basins and estuaries) ............................................................................... 49 3.1.4.4. Riparian, wetland and mangrove/saltmarsh extent (freshwater basins and estuaries) ...... 51 3.1.5. Fish ........................................................................................................................................ 51 3.2. Inshore and Offshore condition assessment ................................................................................ 52 3.2.4. Inshore water quality ............................................................................................................ 52 3.2.4.1. Nutrients, chlorophyll-a, water clarity and pesticides .......................................................... 52 3.2.4.2. Pesticides .............................................................................................................................. 56 3.2.5. Offshore Water Quality ......................................................................................................... 57 3.2.6. Coral ...................................................................................................................................... 59 3.2.7. Inshore seagrass .................................................................................................................... 60 3.2.7.1. Marine Monitoring Program ................................................................................................. 60 3.2.7.2. Queensland Ports Seagrass Monitoring Program ................................................................. 61 3.2.7.3. Revised method for calculating seagrass scores in Mackay-Whitsunday-Isaac report card 62 3.2.7.4. Combined display approach for MMP and QPSMP seagrass indicators ..............................