With a rising world population and pressure on ecosystems due to development, researchers need sophisticated and integrated approaches for conducting sustainability research. We outline a mixed methods practical sustainability research framework, defined as an equal-priority social–ecological methodology, whereby both community engagement and integrated biodiversity assessments are constructed to identify sustainability trade-offs. We illustrate the framework’s use for investigating the social–ecological trade-offs between preserving and removing temperate mangroves in New Zealand. We used a multistage mixed methods design with three stages to generate knowledge and identify social–ecological trade-offs. Our case study illustrates an operational approach for local mangrove management and regional coastal sustainability. Working with communities affected by ecosystem change through participatory research proved key to knowledge exchange and colearning.