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Blue food systems are crucial for meeting global social and environmental goals. Both small-scale marine fisheries (SSFs) and aquaculture contribute to these goals, with SSFs supporting hundreds of millions of people and aquaculture currently expanding in the marine environment. Here we examine the interactions between SSFs and aquaculture, and the possible combined benefits and trade-offs of these interactions, along three pathways: (1) resource access and rights allocation; (2) markets and supply chains; and (3) exposure to and management of risks. Analysis of 46 diverse case studies showcase positive and negative interaction outcomes, often through competition for space or in the marketplace, which are context-dependent and determined by multiple factors, as further corroborated by qualitative modeling. Results of our mixed methods approach underscore the need to anticipate and manage interactions between SSFs and aquaculture deliberately to avoid negative socio-economic and environmental outcomes, promote synergies to enhance food production and other benefits, and ensure equitable benefit distribution.