Aquaponics has the potential to produce sustainable, high‐quality food through integration of hydroponics and aquaculture, but its commercialization is stalled by bottlenecks in pest and disease management. We reviewed integrated pest and disease management steps and techniques in hydroponics to qualify as suitable techniques for different aquaponic designs. Non‐chemical prophylactic measures are highly proficient for pest and disease prevention in all designs. Still, the use of chemical control methods remains highly complicated for all systems. We simulated 10–20% runoff concentrations of 9 pesticides in the common UVI design and compared them with NOEC, LC50 of fish. Endosulfan seems most toxic with runoff AI (20.7 μg L−1) exceeding LC50 (10.2 μg L−1) and NOEC (0.05 μg L−1). At 20% runoff, most chemical pesticides pose risks in aquaponic systems. Natural pesticides were also discussed as potential alternatives with low acute toxicity to fish, but little is known about their effects on water and bacteria. While insecticides and herbicides are replaceable by well‐established commercial biocontrol measures, fungicides and nematicides would still be relevant in aquaponics due to low efficiency of alternatives (e.g. natural enemies, entomopathogenic fungus). Monitoring and cultural control are the first approaches to contain pest population below the action threshold. Biological controls, in general, are adaptable to a larger extent. Further studies are required on how to utilize indigenous microbial community in aquaponics (dominated by Proteobacteria; effective at ~103–109 CFU mL−1) as a frontline defence.