This study aimed to evaluate the economic and operational performance of three types of biofilter media: bio media, drip irrigation pipes, and polyvinyl chloride (PVC) corrugated pipes in three identical aquaponic systems. Each system included a plastic tank for rearing the Nile tilapia (Oreochromis niloticus), stocked with 160 fish per m³. Water from the fish tank was channeled through a mechanical filter, followed by a biological filter, and then to the hydroponic component (mint cultivation). The design followed the deep water culture (DWC) method, with water ultimately flowing to a sump tank before returning to the fish tank. Key performance metrics included total ammonia nitrogen (TAN) removal efficiency, feed conversion ratio (FCR), plant growth, and long-term economic sustainability. The TAN removal efficiency in the bio media system was significantly the highest (P< 0.05), at 47.59 ± 0.01g/ m³/ day. Drip irrigation pipes showed the lowest performance, removing only 16.80 ± 1.07 g/m³/day. In addition, the bio media system had the best FCR, with the lowest value (P< 0.05) at 1.16 ± 0.01, indicating superior feed efficiency. In terms of plant growth, the bio media system produced the most leaves (720.00 ± 17.32 leaves), reached the tallest height (85 ± 3.46cm), and had the highest fresh biomass (300.00 ± 17.32g), all significantly higher than the other media types. Although the bio media system had the highest initial cost, it delivered superior performance in water quality management, fish growth, and plant productivity, resulting in a more cost-effective solution over time. Drip irrigation pipes, while the cheapest option, led to higher long-term costs due to their lower efficiency in TAN removal and poor feed conversion efficiency. PVC corrugated pipes provided moderate performance. This study suggests that bio media is the optimal choice for commercial aquaponic systems based on its long-term economic benefits.