Optimizing production in aquaponics requires in-depth knowledge of the plant, fish and microbial compartments. This opinion paper is focused on root-released organic compounds and their implication in aquaponics, an area that has received little to no direct research to date. Key scientific literature from two distinct fields of study—phytochemicals in aquaculture science and root exudates in plant science—reveals possible pathways and effects. Root exudates, passively or actively released by plants as a stress response, protection or signalling, have the potential to influence the systems microbiome and the cultured fish, as similar phytochemicals have been found to affect bacterial abundance and diversity and fish health and behaviour. These are key aspects to run aquaponics successfully, which shows the need for further investigation to better understand sources and mechanisms of such molecules and possible ways to harness beneficial effects that can guide new research directions as the role of aquaponics grows in recirculating aquaculture.