Fishmeal is commonly used as a protein source in aquaculture feeds; however, there is a growing need to reduce its use due to sustainability concerns. This study evaluated the proximate composition (crude protein, lipid, fiber, ash, and nitrogen-free extract), palatability, attractability, and water stability of a formulated diet using Spirulina and Azolla as fishmeal replacements, as well as the growth performance of koi carp (Cyprinus carpio var. koi) cultured in an aquaponic system. Three different fishmeal replacement levels were tested: 30% and 50% replacement with Spirulina and Azolla. The parameters measured included weight gain rate (WGR%), specific growth rate (SGR%), survival rate (%), feed efficiency (FE), and feed conversion ratio (FCR). Water quality parameters—temperature, dissolved oxygen, pH, ammonia, nitrite, and nitrate—were monitored weekly. There were no significant differences (P > 0.05) in the proximate composition, attractability, palatability, water stability, or growth performance between the diets containing Spirulina and Azolla and the control diet. Similarly, there were no significant differences (P > 0.05) in the measured water quality parameters. The results indicate that Spirulina and Azolla can successfully replace up to 50% of fishmeal in the formulated diet for koi carp without negatively affecting growth performance or water quality in an aquaponic system.