The experiment was aimed at standardization of water flow rate in aquaponic system in order to correlate nutrient removal and water quality with growth of Cyprinus carpio var. koi (koi carp fingerlings) and Beta vulgaris var. bengalensis (spinach). Different flow rates, i.e., 3.2, 1.5, and 1.0 l min−1, were assigned as treatments T1, T2, and T3, respectively, with spinach plants (28 plant m−2), whereas S1 and S2 were the treatments having flow rates of 1.5 and 1.0 l min−1, respectively, without plants. Control (C) was set at flow rates of 3.2 l min−1 without plants. Treatment T2 (1.5 l min−1) showed highest weight gain of koi carp fingerlings and also height gain of spinach plants as compared to other treatments. There was no significant difference in length gain, percentage weight gain, specific growth rate, feed conversion ratio, feed efficiency ratio, and protein efficiency ratio as compared to other treatments and control. All the treatments, T1, T2, and T3, effectively remove nitrate (77–78 %), phosphate (47.04–55.06 %), and potassium (22.85–29.16 %) from fish effluent tanks. These results suggest that flow rates 3.2, 1.5, and 1.0 l min−1 were effective under aquaponic system. Of which, 1.5 l min−1 can be suggested as optimum water flow rate for the growth of spinach and koi carp in aquaponic system as percentage weight gain in fish, percentage height gain, and yield of plants were higher compared to flow rates 3.2 and 1.0 l min−1.