Aquaponics is the combined cultivation of fish in aquaculture systems and plants in hydroponic systems (HPS). This study aimed to explore and evaluate new aquaponics system designs in Jakarta, Indonesia, in terms of water and nutrient efficiency, and/ or profitability. The systems are combination of recirculated aquaculture system, HPS, duckweed cultivation system, and anaerobic digester units. The latter converted settled material from RAS to biogas and waste sludge. In total, one brackish water (BW) system with barramundi-tomato and three freshwater (FW) systems with Nile tilapia-rice-duckweed, Nile tilapia-rice, and Nile tilapia-tomato were investigated using dynamic mathematical models using mass balance. State variables included are fish biomass, feed, plant biomass, phosphorus, NH4+, and NO3-. The results showed an increase of N, P, and water use efficiency by 10%, 18%, and 31%, respectively, in FW system of Nile tilapia-rice compare to Nile tilapia-tomato. Meanwhile, adding duckweed in the Nile tilapia-rice FW system only contribute a slight increase of nutrient and water the efficiency while worsened the already negative net present value (NPV) of the system due to the high land prices in Jakarta. The BW system had similar water and nutrient efficiency to FW system of Nile tilapia-tomato, but a lower NPV. Profit of the Barramundi-tomato and Nile tilapia-tomato becomes comparable if the hydroponic area in the former system can be expanded by 35%, or the selling price of tomato or fish can be increased by 20%. Given the expected growth of both the production of tomatoes and aquaculture in Indonesia, there is potential for further introduction of aquaponics systems in Indonesia.