A multi-sectoral assessment of risks can support the management and investment decisions necessary for emerging blue economy industries to succeed. Traditional risk assessment methods will be challenged when applied to the complex socio-ecological systems that characterise offshore environments, and when data available to support management are lacking. Therefore, there is a need for assessments that account for multiple sectors. Here we describe the development of an efficient method for an integrated hazard analysis that is a precursor to full risk assessments. Our approach combines diverse disciplinary expertise, expert elicitation and multi-criteria analysis to rank hazards, so it encompasses all types of hazards including human-caused, natural and technological. We demonstrate our approach for two sectors that are predicted to grow rapidly in Australia: offshore aquaculture and marine renewable energy. Experts ranked Climate Change as the hazard with the highest overall concern, but hazards including Altered Ecosystem Function, Biosecurity, Cumulative Effects, Structural Failure and Social Licence were also highly ranked. We show here how outputs from this approach (multi-criteria scores and ranks) could be used to identify hazards that; i) could be safely retired, ii) should be progressed to more quantitative risk assessments or iii) require ongoing information collection. The approach can encompass all types of hazards, which enables it to holistically consider priorities. The expert-based multi-criteria approach outlined here represents a pragmatic way to solve some of the challenges of applying risk assessments to emerging industries by using a method that can be applied across multiple blue economy sectors.