Although agriculture and aquaculture depend on access to increasingly scarce, shared water resources to produce food for human consumption, they are most often considered in isolation. We argue that they should be treated as integrated components of a single complex system that is prone to direct or indirect tradeoffs that should be avoided while also being amenable to synergies that should be sought. Direct tradeoffs such as competition for space or the pollution of shared water resources usually occur when the footprints of agriculture and aquaculture overlap or when the two practices coexist in close proximity to one another. Interactions can be modulated by factors such as hydropower infrastructure and short-term economic incentives, both of which are known to disrupt the balance between aquaculture and agriculture. Indirect tradeoffs, on the other hand, play out across distances, i.e., when agricultural food sources are diverted to feed animals in aquaculture. Synergies are associated with the culture of aquatic organisms in rice paddies and irrigation waters, seasonal rotations of crop cultivation with aquaculture, and various forms of integrated agriculture–aquaculture (IAA), including jitang, a highly developed variant of pond-dike IAA. Policy decisions, socioeconomic considerations, and technology warrant increased scrutiny as determinants of tradeoffs and synergies. Priority issues for the future include guiding the expansion of aquaculture from its traditional base in Asia, taking advantage of the heterogeneity that exists within both agricultural and aquaculture systems, the development of additional metrics of tradeoffs and synergies, and adapting to the effects of climate change.