The present work evaluated the capability of Arthrospira platensis complete biomass (ACDW) and the lipid-free biomass (LFB) to remove ammonium ions (NH4+) from aquaculture wastewater discharge. Under controlled conditions in flasks filled with 100 mL of distilled water (synthetic aqueous solution), a batch process ion-exchange was conducted by changing the main parameters including contact times (15, 30, 45, 60, 120, and 180 min), initial ammonium ion concentrations (10, 20, 30, 40, 50, and 100 mg·L−1), and initial pH levels (2, 4, 6, 8, and 10) at various dosages of ACDW and LFB as adsorbents (0.02, 0.04, 0.06, 0.08, and 0.1 g). After lab optimization, ammonia removal from real aquaculture wastewater was also examined. The removal of ammonium using ACDW and LFB in the synthetic aqueous solution (64.24% and 89.68%, respectively) was higher than that of the real aquaculture effluents (25.70% and 37.80%, respectively). The data of IR and Raman spectroscopy confirmed the existence of various functional groups in the biomass of ACDW and LFB. The adsorption equilibrium isotherms were estimated using Freundlich, Langmuir, and Halsey models, providing an initial description of the ammonia elimination capacity of A. platensis. The experimental kinetic study was suitably fit by a pseudo-second-order equation. On the other hand, as a result of the treatment of real aquaculture wastewater (RAW) using LFB and ACDW, the bacterial counts of the LFB, ACDW, ACDW-RAW, and RAW groups were high (higher than 300 CFU), while the LFB-RAW group showed lower than 100 CFU. The current study is the first work reporting the potential of ammonia-loaded microalgae biomass as a feed source for the rotifer (Brachionus plicatilis). In general, our findings concluded that B. plicatilis was sensitive to A. platensis biomass loaded with ammonia concentrations. Overall, the results in this work showed that the biomass of A. platensis is a promising candidate for removing ammonia from aquaculture wastewater.