Aquaponics is the combination of aquaculture and hydroponic technology to grow fish and plants together. While aquaponics can play a role in food security, it may also be a potential educational tool because of its interdisciplinary nature and required technological skills. With aquaponics, students could conduct activities involving chemistry, physics, biology and sustainability to solidify their understanding of scientific theories. The interdisciplinary nature of aquaponics may make it an appealing tool for science education, yet that same aspect may also make an aquaponics system challenging to implement and manage. Given this paradox, this exploratory research assessed challenges and solutions facing aquaponics in education with a focus on implementation. In-depth interview data were collected through phone interviews with educators (N = 10) who currently, or had in the past five years, used an aquaponics system in educational settings in North America. Participants reported two challenges: technical difficulties as a result of the nature of aquaponics and restrictions as a result of school settings. Solutions given by participants were physical aquaponics system modifications and the development of community connections and support, passion for aquaponics and expertise. These findings will help educators manage their expectations for aquaponics while establishing objectives for their individual settings.