This study aims to investigate the nexus between small-scale freshwater aquaculture and poverty-related factors like income generation and food security in rural Madagascar. Evidence of this relationship is scarce in the Global South, particularly in island states. Using linear and logistic regressions and data collected from fish farmers and consumers across six regions in Madagascar in 2021, we obtained significant findings. Extension services, integrated production systems, and higher education are positively correlated with fish-based income generation. For instance, membership in a cooperative can double an aquaculture farmer’s total annual income compared to that of other producers. Wealth is a key determinant of food security, but female decision-makers, fish consumption, and education are also positively correlated with food security. These insights emphasize the vital roles of small-scale aquaculture and women in the household in enhancing livelihoods and food security, underscoring the need for targeted support and policy interventions to foster inclusive and resilient freshwater aquaculture in island states.