The deep sea remains one of the least explored ecosystems on the planet, with 95% still uncharted. From what is known, it harbours critical habitat-forming species like cold-water corals and sponges that sustain extraordinary biodiversity and provide key ecosystem services, including supporting fisheries. These fragile ecosystems face escalating threats from climate change and bottom trawling, yet the extent of their impacts remains poorly understood. This PhD addresses these gaps by examining how these stressors influence Vulnerable Marine Ecosystem (VME) indicator taxa in New Zealand’s Exclusive Economic Zone and explores implications for conservation. The research explores (i) climate change impacts and potential refugia, (ii) the added pressure of bottom trawling, and (iii) management strategies with policymakers and fishery regulators to fast-track spatial protection measures in the New Zealand region. In Chapter 2, species distribution models were used to predict the spatial distribution of density for several deep-water VME indicator taxa under present-day environmental conditions and two future climate scenarios (SSP2-4.5 and SSP3-7.0) projected by the end of the 21st century. Results showed a significant decline in both the density (54%) and spatial extent (61%) of all assessed taxa under future conditions compared to the current day. However, the models also identified potential climate refugia: areas where certain taxa may persist despite changing environmental pressures, representing crucial conservation targets. This and previous research, however, indicate that existing spatial management measures with respect to bottom trawling may be insufficient to protect VME indicator taxa now and into the future. This suggests that present-day densities, even within potential climate refugia areas, may have already declined due to this activity. Chapter 3 examines the impact of bottom trawling by estimating the density loss of VME indicator taxa in high-density areas, particularly climate refugia, in New Zealand waters over the past 30 years. Bottom trawling was predicted to have reduced the current density of all assessed taxa across the study region, with the most pronounced reductions in taxon density and habitat extent (up to 10% loss) occurring in areas predicted to be climate refugia. Such declines may undermine the ability of taxa to form ecologically functional habitats in the future if these impacts persist. The interplay between climate change and bottom trawling presents a complex multi-stressor scenario for VMEs and their indicator taxa. Addressing these cumulative impacts requires integrated approaches that simultaneously consider ecological and social dimensions to provide the scientific knowledge required to support management decisions. Chapter 4 introduces a social-ecological perspective by combining density-based spatial analysis of VME indicator taxa distributions under multiple stressors (e.g., climate change and bottom trawling) with participatory methods, including interviews and group elicitation with policy regulators and fishery experts. This approach aimed to assess risk perceptions, inform potential management actions, and identify barriers and solutions for effective conservation in the New Zealand region. Findings revealed that presenting additional scientific evidence and engaging a diverse group of stakeholders in discussions enhanced their risk perceptions and confidence about the impacts of climate change and bottom trawling on VME indicator taxa. Additionally, stakeholder engagement helped refine potential strategies for implementing spatial management measures. By adopting a social-ecological approach, this PhD thesis integrated ecological modelling, spatial impact analysis, and participatory methods to provide insights into the multiple effects of climate change and bottom trawling on VME indicator taxa and their effective management. The findings that originated from this work can contribute to the development of climate-resilient marine spatial planning strategies aimed at strengthening the long-term protection of deep-sea VMEs as well as from additional impacts such as bottom trawling. Moreover, the thesis identifies key scientific knowledge gaps, including the need for connectivity analyses and recovery following disturbance from local stressors such as bottom trawling. This information can be useful to enhance the predictive power of species distribution models and the importance of broader stakeholder involvement—particularly the fishing industry—to facilitate the implementation of management initiatives in a socially just and equitable manner.