Water, energy and food insecurity and precarity, synthesised as the Water-Energy-Food (WEF) Nexus, highlight the need for creative imagining, using a transdisciplinary approach to engage critically with these complex problems. To discover and understand the imaginations and innovations that could steer us to a sustainable future, we propose to work in very local, urban contexts, where WEF challenges reflect the legacies of Apartheid and colonialism. Through community engagement and citizen science labs, we will use a case study of systems thinking in practice to advance socio-political understandings of responses to complex, interconnected but spatially and temporally dispersed problems, and critique discourses of resilience, resourcefulness and sustainability. Citizen Eco-Labs and Art-Labs in Johannesburg (Gauteng), Mankweng (Limpopo), and Alice and East London (Eastern Cape) will enable us to describe community-based understandings of WEF precarity and its particular impact for women and youth. We will generate new knowledge of responses and actions to such precarity, and analyse how ongoing collaborations among community members, local organisations, and multiple public and private partners enable socially inclusive, eco-cultural responses to the environment. We aim to work with local residents and draw on their understandings of the WEF-Nexus, through participatory methods of engagement, to develop guidelines for best practice for partnerships that can contribute to improving livelihoods, the environment and wellbeing.