Aquaculture has emerged as a key sector in addressing global food shortages, contributing to 50% of the world’s food production. However, to prevent infections and diseases of the produced aquatic organisms, like mollusks and fish, and improve their reproductivity, chemicals such as antibiotics, pesticides, and hormones are used. Since these substances are not completely absorbed, they remain in the water, generating large volumes of contaminated wastewater (around 200,000 m3 annually), with significant environmental challenges due to their persistence. As they cannot be removed by conventional treatments, sustainable advanced technologies that can effectively eliminate them are urgently needed. This study explores a sustainable solution using a waste-based zero-valent iron (ZVI) catalyst derived from olive mill wastewater (OMW, SMALLOPS S.L.) for aquaculture wastewater treatment. The research aimed to evaluate the efficacy of a waste-based solar ZVI photocatalytic process for degrading persistent microcontaminants (MCs) in a simulated aquaculture wastewater matrix. The MCs targeted in this study included Sulphapyridine, Trimethoprim, Caffeine, Sulfamethoxazole, and Flumequine at 100 µg/L of each and circumneutral pH. The catalyst used was an innovative iron nanoparticle with a particle size of 150 nm ± 50 nm and a surface area of 14.7 m2/g, containing 44.5% of total iron and 2.5% of ZVI, according to the manufacturer (SMALLOPS S.L., in Spain). Experiments were conducted using two reactor systems: a 2L Borosilicate Glass Reactor (BGR) and a 17L Raceway Pond Reactor (RPR) at Plataforma Solar de Almeria (PSA-CIEMAT) in Spain. Both systems operated under natural solar radiation in the presence of hydrogen peroxide (H2O2) at 3 and 5 mM. The goal was to achieve at least 50% degradation of the mixture of the 5 MCs. Results showed that the borosilicate glass reactor achieved the target degradation of 50% after 45 min (0.80 kJ/L of accumulated UV radiation), while in the RPR, 40% degradation was achieved in 60 min (2.04 kJ/L). The H2O2 consumption was 4 mg/L in the borosilicate reactor and 7 mg/L in the RPR. Persistence analysis of the contaminants revealed that Caffeine was the most resistant to degradation, followed by Sulfamethoxazole, Trimethoprim, Sulphapyridine, and Flumequine with H2O2 at three mM. Increasing the concentration of H2O2 from 3 mM to 5 mM did not significantly enhance the photodegradation rates. Between 1 and 3 mg/L of iron leaching from the catalyst was measured in this study, but it was demonstrated that the levels of dissolved iron in the solution had a negligible effect on MC degradation via the Fenton like process.