A methodology to assess river habitat quality : a thesis presented in partial fulfilment of the requirements for the degree of a Masters in Science in Ecology at Massey University, Manawatū, Aotearoa New Zealand

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Declines in the ecological health of rivers and streams worldwide have led to a range of policy responses from environmental protection organisations and government departments. However, while policy has often provided specific direction on issues such as nutrient and sediment pollution, over-abstraction of water, flow regulation, and (increasingly) the impacts of climate change, direction to protect the condition of physical habitat in rivers and streams has been vague at best—despite its wide recognition as a core component of ecosystem health. In Aotearoa New Zealand, protection of the 'natural character' of rivers and the 'habitats of indigenous freshwater species' is required under the Resource Management Act (1991) and National Policy Statement for Freshwater Management (2020), however, very few regional authorities effectively manage physical habitat, and regulations have so far not stopped ongoing declines in habitat condition. While a range of methods have been developed to assess and monitor the condition of physical habitat in rivers and streams, many are complex or conflate variables and there is little to suggest any have been effectively applied in resource management to reverse ongoing habitat degradation. This thesis explores this issue, considering what makes a robust and effective ecological assessment of physical habitat, reviewing a range of existing assessment techniques against those criteria, exploring the opportunity to improve habitat quality assessment through the integration of readily available drone technology, and testing the efficacy of drone integration in the field. I find that Death et al.'s 'Habitat Quality Index' (HQI) has considerable value as an assessment of change in habitat quality, evaluate the efficacy of visually assessing fine sediment cover and substrate composition using a drone, present a comprehensive hybrid HQI assessment of native fish habitat in a reach of river subject to in-stream engineering works, and discuss the implications of using drones for physical habitat assessment.