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The aquaponic system is an alternative strategy to treat aquaculture waste and achieve food independence. Bacteria play vital roles in the aquaponic system as they can transform ammonia or ammonium into nitrite and then into nitrate, which is more favorable for bacteria, fish, and plants. The objective of this study was to determine the effect of nitrifying bacteria (Nitrosomonas europaea Winogradsky and Nitrobacter winogradskyi Winslow) on the aquaponic system in terms of water quality, nutrient availability, and productivity of carp (Cyprinus carpio), lettuce (Lactuca sativa var. crispa), and vetiver grass (Chrysopogon zizanioides L.). The experiment consisted of four treatments: aquaculture of carp as a control for fish (A), hydroponic of lettuce and vetiver grass without nutrient addition as a control for plants (B), aquaponic (carp, lettuce, vetiver grass) (C), and aquaponic with nitrifying bacteria addition (D). The results showed nitrifying bacteria addition had a significant effect on daily growth rate (DGR) and relative growth rate (RGR) of lettuce within a treatment; on the other hand, the nitrifying bacteria did not give a significant effect to RGR of vetiver grass. The growth rate, specific growth rate, and survival rate of the carp in aquaculture treatment (A) were lower than in both aquaponic treatments (C and D). Nitrifying bacteria addition in the aquaponics system had a significant effect of increasing the orthophosphate concentration. Water quality was also indicated to be better in the aquaponic system than in the aquaculture system. The integration of aquaculture and hydroponics with the addition of nitrifying bacteria enables the formation of microorganism communities, nitrate, and orthophosphate, which lead to the improvement of water quality, nutrient availability, and plant growth.