The deep sea could soon become Earth's largest mining frontier. Seafloor mineral deposits host vast quantities of metals which are necessary to transition away from fossil fuels towards an affordable and clean energy future. Polymetallic nodules are potato-sized mineral concretions that form on the deep ocean floor. They are often found in high abundance on abyssal plains at water depths between three and six kilometres. Located in the central Pacific Ocean, the Clarion-Clipperton Zone is home to some of Earth's largest deposits of energy transition metals, with over one million km2 of active exploration licenses for polymetallic nodules. These nodules consistently contain high concentrations of multiple metal commodities, such as nickel, cobalt, copper and manganese, which are essential ingredients in emerging clean energy technologies. Many of these metals face future supply risks, especially in high-demand scenarios that align with decarbonisation goals. Regulations and guidelines for deep-sea mining of polymetallic nodules are nearing completion, including rules to ensure the effective protection of the marine environment. However, several governments, non-government organisations, and businesses have become increasingly concerned about potential risks to deep-sea ecosystems and uncertainty regarding environmental management practices. First, this thesis proposes a framework for effective environmental management of polymetallic nodule mining based on a review of scientific literature. The framework identifies key drivers, barriers, and enablers to effective management, emphasising the importance of the precautionary approach, ecosystem approach, and adaptive management. Second, adaptive management is identified as an essential tool for dealing with new information, reducing uncertainty, and improving environmental management practices. A conceptual framework for adaptive management is proposed, highlighting the role of participatory modelling to engage experts and develop environmental management and monitoring plans. Third, a methodology for environmental risk assessment is proposed to identify, analyse, and evaluate the potential environmental effects of deep-sea mining. The methodology is tailored to the complexity and uncertainty associated with deep-sea environments and ensures that assessments are fit-for-purpose, informing management decisions throughout the environmental impact assessment process. Fourth, an open-source ecosystem modelling software package was developed to analyse the structure and function of complex and data-limited ecosystems. The software enables the development of informative indicators to assess and monitor the environmental effects of deep-sea mining activities. Finally, the culmination of this thesis is an integrated ecosystem assessment which synthesises current knowledge of ocean and seafloor ecosystems in the Clarion-Clipperton Zone based on an ecosystem model developed during two expert workshops. The model reveals the key components and processes that regulate ocean and seafloor ecosystems and is used to identify potential risks to ecosystem functions and services from mining pressures. The assessment highlights informative indicators and mitigation measures, forming the basis for quantitative risk assessments as data from baseline studies and test mining becomes increasingly available. The main novel contributions of this research are as follows. The thesis proposes that multiple environmental risk assessments are needed to account for inherent trade-offs in risk assessment methods and inform each stage of the environmental impact assessment process for deep-sea mining. The modelling software enables the participatory development of an ecosystem model for the Clarion-Clipperton Zone, providing a working hypothesis of deep-sea ecosystem structure and function and a scientific basis for adaptive management. The thesis highlights that coupling this ecosystem model with adaptive management strategies creates a formalised and iterative learning process that could help resolve uncertainties about the environmental risks of deep-sea mining. The subsequent integrated ecosystem assessment reveals the underlying drivers of pelagic and benthic ecosystem processes and, notably, found no direct or indirect causal pathways from the abyssal seafloor to upper ocean ecosystems in the Clarion Clipperton Zone, highlighting promising new measures for ecosystem-based management. This thesis presents timely scientific contributions amidst accelerating industry and regulatory progress, as well as increasing public interest in the environmental, social and governance issues surrounding deep-sea mining. This research aims to inform ecologically responsible mining practices to improve outcomes for nature and human development. The thesis highlights that over the coming years, there is an opportunity to implement proactive, rather than reactive, measures for effective environmental management to conserve deep-sea ecosystems before the likely onset of commercial deep-sea mining.