Resilience deals explicitly with change and provides a middle ground between the social and the environmental sciences. However, a growing critique by social scientists questions the ability of resilience thinking to adequately examine the social dimensions of change. The question that emerges is how social scientists should engage with resilience. We addressed this question by comparing resilience with agrarian change and transitions theory, through the backdrop of the fastest growing global food sector, aquaculture. Our analysis showed that each theoretical perspective provides fundamentally different insights into social and environmental transition inherent in the aquaculture sector. Although resilience thinking is best suited to assessing the ecological aspects of production, its systems ontology limits the inclusion of dynamic social relations or innovation. In contrast, agrarian transition enables a more meaningful understanding of how social relations are reconfigured as agrarian society shifts toward more capitalist modes of production, and transitions theory provides insights into social process of innovation. Given the epistemological differences between these theoretical approaches, we argue against attempts that reify systemic thinking by naturalizing social theories and concepts into resilience thinking. Instead, we argue that social theories such as agrarian change and transition theory should be seen as complimentary and that integration should focus on bridging results and insights. Doing so enables a more robust assessment of the social aspects of social-ecological transitions in the aquaculture sector and beyond.