Aquaponic effluent is increasingly recognized as a sustainable alternative to traditional hydroponics due to its rich microbial content, which can enhance nutrient and water uptake efficiency in industrial hemp (Cannabis sativa). This research aimed to identify the minimum threshold of aquaponic effluent required to maintain an established microbial community while providing comparable benefits to plant growth and resource use efficiency. Three treatments of aquaponic effluent were applied to industrial hemp: (1) 90% hydroponic and 10% aquaponic nutrient solution, (2) 100% hydroponic nutrient solution with a 1 day 100% aquaponic treatment (once per week), and (3) 100% hydroponic nutrient solution with a 1 day biweekly 100% aquaponic treatment. Results indicated that in all cases, aquaponic effluent led to increased nutrient and water uptake efficiency in cannabis plants, demonstrating that even a small inclusion of aquaponic effluent can substantially improve plant performance. The 90% hydroponic, 10% aquaponic treatment showed the highest water use efficiency and greatest terpene diversity. This threshold identification provides a bridge to future innovations in utilizing aquaponic effluent for commercially produced crops.