Increasing anthropogenic pressure on the sea and alteration of coastscapes challenge the functioning of marine ecosystems and long-term reliance on blue economies, especially for developing southern economies. The structural hardening of shores can result in ecological disruptions, with cascading effects on the wellbeing and livelihoods of marginalised groups who depend on marine resources. Mitigation, adaptation and rehabilitation options for coastal developments should include innovative, socially responsible solutions to be used to modify shorelines and ensure long-term functionality of metropolitan coastal ecosystems. Nature-based innovations are being developed to improve surrogacy for natural marine ecosystems. The co-creation of nature-based structures, entailing partnerships between scientists and a local rural community is currently being considered in South Africa and we present this regional case study as a transdisciplinary framework for research in nature-based, ecological engineering of coastal systems. Novel transdisciplinary approaches include ecomusicological interventions, where traditional cultural expressions (TCEs) create opportunities for transgressive pedagogy. This step aims to ensure that the knowledge gathered through nature-based scientific research remains a part of community developed Indigenous knowledge systems. The merging of innovative, eco-creative approaches and TCEs has the potential to sustainably and ethically improve the functioning and diversity of coastal urban habitats. This review tackles the potential of transdisciplinary settings to transform urban coastlines using “low-tech” engineering and Indigenous eco-creative innovations to pedagogy, to benefit the people and biological communities as well as reduce social and gender inequalities.