Aquaponic systems are made up of hydroponic beds and recycled aquaculture systems. The significant elements that determine how effectively an aquaponic system operates are the nitrogen cycle (nitrification) and the phosphorus cycle (phosphate). Because some research indicates that aquaponics systems are primarily deficient in phosphorus, phosphate-enriched nutrients were added to raise the phosphorus levels. During an eight-week experimental period, the effects of water quality parameters and microbiology, animal and plant growth performance, chlorophyll compounds in lettuce, and the bacterial community were analyzed. Phosphate concentration (1.604 ± 1.933 mg L⁻¹) and ammonia-oxidizing bacteria (AOB) (1.19 × 10² ± 1.30 CFU mL⁻¹) give significant positive reactions to the added nutrients. However, the prawn survival rate (17.00 ± 0.63%) showed a significantly negative response to nutrition modification containing phosphate, and the percentage of bacterial pathogens became more dominant (pathogen 40.51%; N_bacteria 35.05%; probiotics 24.44%). This study shows that adding phosphate increases phosphorus levels in an aquaponics system and changes the microbial community and species growth performance.